Starting phenix.real_space_refine on Fri Jan 17 20:03:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xih_38373/01_2025/8xih_38373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xih_38373/01_2025/8xih_38373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xih_38373/01_2025/8xih_38373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xih_38373/01_2025/8xih_38373.map" model { file = "/net/cci-nas-00/data/ceres_data/8xih_38373/01_2025/8xih_38373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xih_38373/01_2025/8xih_38373.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 7326 2.51 5 N 1941 2.21 5 O 2091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11418 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4744 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 25, 'TRANS': 553} Chain breaks: 4 Chain: "B" Number of atoms: 6020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6020 Classifications: {'peptide': 735} Link IDs: {'PTRANS': 33, 'TRANS': 701} Chain breaks: 4 Chain: "G" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "H" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 337 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.71, per 1000 atoms: 0.59 Number of scatterers: 11418 At special positions: 0 Unit cell: (102, 94.35, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 31 15.00 Mg 2 11.99 O 2091 8.00 N 1941 7.00 C 7326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 33.6% alpha, 18.5% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.615A pdb=" N VAL A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.694A pdb=" N ASN A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.546A pdb=" N ARG A 369 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 406 through 423 Processing helix chain 'A' and resid 442 through 451 removed outlier: 4.162A pdb=" N ILE A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.733A pdb=" N ARG A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 528 through 546 Processing helix chain 'A' and resid 603 through 624 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.579A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.969A pdb=" N TYR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 4.168A pdb=" N VAL B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 243 through 250 removed outlier: 3.670A pdb=" N HIS B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.582A pdb=" N ARG B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 405 through 423 Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.645A pdb=" N ILE B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 528 through 546 Processing helix chain 'B' and resid 579 through 582 removed outlier: 4.052A pdb=" N GLU B 582 " --> pdb=" O LYS B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 602 through 624 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 640 through 657 Processing helix chain 'B' and resid 735 through 748 Processing helix chain 'B' and resid 761 through 770 Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.557A pdb=" N GLN A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 217 removed outlier: 4.284A pdb=" N ARG A 286 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 359 removed outlier: 5.091A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A 353 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 467 Processing sheet with id=AA8, first strand: chain 'A' and resid 507 through 509 Processing sheet with id=AA9, first strand: chain 'A' and resid 584 through 590 removed outlier: 6.722A pdb=" N ILE A 561 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 633 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 563 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASP A 635 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 565 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 731 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP A 670 " --> pdb=" O MET A 729 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N MET A 729 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS A 672 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A 727 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 698 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AB2, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.650A pdb=" N GLN B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AB4, first strand: chain 'B' and resid 79 through 82 Processing sheet with id=AB5, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.691A pdb=" N SER B 267 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 325 through 326 removed outlier: 4.020A pdb=" N LEU B 325 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 356 through 359 removed outlier: 4.885A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 353 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 395 through 398 removed outlier: 3.941A pdb=" N ILE B 432 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 465 through 467 Processing sheet with id=AC1, first strand: chain 'B' and resid 507 through 509 removed outlier: 3.850A pdb=" N ARG B 522 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 584 through 590 removed outlier: 3.505A pdb=" N ILE B 561 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 635 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL B 567 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 630 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 669 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE B 632 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 671 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG B 634 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 726 " --> pdb=" O HIS B 672 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3217 1.34 - 1.46: 2408 1.46 - 1.58: 6027 1.58 - 1.70: 59 1.70 - 1.82: 46 Bond restraints: 11757 Sorted by residual: bond pdb=" N MET B 403 " pdb=" CA MET B 403 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.23e-02 6.61e+03 4.55e+00 bond pdb=" C3' DG H 12 " pdb=" O3' DG H 12 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.51e+00 bond pdb=" N ASN A 580 " pdb=" CA ASN A 580 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.46e+00 bond pdb=" C ILE B 84 " pdb=" N PRO B 85 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.36e+00 bond pdb=" CG PRO B 71 " pdb=" CD PRO B 71 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.80e+00 ... (remaining 11752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 15729 2.21 - 4.41: 238 4.41 - 6.62: 33 6.62 - 8.82: 7 8.82 - 11.03: 1 Bond angle restraints: 16008 Sorted by residual: angle pdb=" CG ARG B 128 " pdb=" CD ARG B 128 " pdb=" NE ARG B 128 " ideal model delta sigma weight residual 112.00 120.29 -8.29 2.20e+00 2.07e-01 1.42e+01 angle pdb=" N LYS A 579 " pdb=" CA LYS A 579 " pdb=" C LYS A 579 " ideal model delta sigma weight residual 110.35 115.43 -5.08 1.36e+00 5.41e-01 1.40e+01 angle pdb=" CB MET A 737 " pdb=" CG MET A 737 " pdb=" SD MET A 737 " ideal model delta sigma weight residual 112.70 123.73 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA GLU A 337 " pdb=" CB GLU A 337 " pdb=" CG GLU A 337 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 angle pdb=" C3' DG H 12 " pdb=" O3' DG H 12 " pdb=" P DT H 13 " ideal model delta sigma weight residual 120.20 125.08 -4.88 1.50e+00 4.44e-01 1.06e+01 ... (remaining 16003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6590 35.97 - 71.94: 357 71.94 - 107.90: 11 107.90 - 143.87: 3 143.87 - 179.84: 4 Dihedral angle restraints: 6965 sinusoidal: 3093 harmonic: 3872 Sorted by residual: dihedral pdb=" C4' DG H 12 " pdb=" C3' DG H 12 " pdb=" O3' DG H 12 " pdb=" P DT H 13 " ideal model delta sinusoidal sigma weight residual -140.00 39.84 -179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG H 15 " pdb=" C3' DG H 15 " pdb=" O3' DG H 15 " pdb=" P DT H 16 " ideal model delta sinusoidal sigma weight residual 220.00 54.66 165.34 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG H 4 " pdb=" C3' DG H 4 " pdb=" O3' DG H 4 " pdb=" P DG H 5 " ideal model delta sinusoidal sigma weight residual 220.00 72.02 147.98 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 6962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1445 0.055 - 0.110: 242 0.110 - 0.166: 48 0.166 - 0.221: 6 0.221 - 0.276: 2 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CB ILE B 84 " pdb=" CA ILE B 84 " pdb=" CG1 ILE B 84 " pdb=" CG2 ILE B 84 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CG LEU A 8 " pdb=" CB LEU A 8 " pdb=" CD1 LEU A 8 " pdb=" CD2 LEU A 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PRO A 491 " pdb=" N PRO A 491 " pdb=" C PRO A 491 " pdb=" CB PRO A 491 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.61e-01 ... (remaining 1740 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 70 " -0.058 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 71 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 71 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 71 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 490 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO A 491 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 337 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO B 338 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.030 5.00e-02 4.00e+02 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 112 2.62 - 3.19: 9208 3.19 - 3.76: 17252 3.76 - 4.33: 23344 4.33 - 4.90: 39542 Nonbonded interactions: 89458 Sorted by model distance: nonbonded pdb=" OP1 DA H 3 " pdb="MG MG H 101 " model vdw 2.044 2.170 nonbonded pdb=" OP2 DT G 0 " pdb="MG MG G 101 " model vdw 2.085 2.170 nonbonded pdb=" OP2 DT H 1 " pdb="MG MG H 101 " model vdw 2.259 2.170 nonbonded pdb=" OG SER B 50 " pdb=" O GLY B 55 " model vdw 2.263 3.040 nonbonded pdb=" O ASN B 290 " pdb=" NH2 ARG B 295 " model vdw 2.268 3.120 ... (remaining 89453 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11757 Z= 0.232 Angle : 0.655 11.026 16008 Z= 0.346 Chirality : 0.046 0.276 1743 Planarity : 0.005 0.085 1922 Dihedral : 20.099 179.842 4467 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.93 % Allowed : 31.18 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1294 helix: 1.23 (0.27), residues: 372 sheet: -0.66 (0.31), residues: 295 loop : -1.95 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 214 HIS 0.004 0.001 HIS A 571 PHE 0.020 0.001 PHE A 481 TYR 0.012 0.001 TYR A 490 ARG 0.011 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: B 195 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8126 (mmm160) REVERT: B 266 MET cc_start: 0.7430 (ptm) cc_final: 0.7182 (ppp) outliers start: 11 outliers final: 3 residues processed: 116 average time/residue: 0.2927 time to fit residues: 47.1598 Evaluate side-chains 109 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 580 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 66 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 568 HIS A 571 HIS B 571 HIS B 580 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105130 restraints weight = 17585.432| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.39 r_work: 0.3087 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 11757 Z= 0.536 Angle : 0.710 7.771 16008 Z= 0.379 Chirality : 0.048 0.199 1743 Planarity : 0.006 0.072 1922 Dihedral : 17.268 169.153 1792 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 5.95 % Allowed : 28.12 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1294 helix: 1.34 (0.27), residues: 380 sheet: -1.06 (0.30), residues: 314 loop : -2.07 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 131 HIS 0.008 0.001 HIS B 571 PHE 0.021 0.002 PHE B 577 TYR 0.014 0.002 TYR A 714 ARG 0.005 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 103 time to evaluate : 1.329 Fit side-chains REVERT: A 2 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7842 (ptpp) REVERT: A 520 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5596 (pm20) REVERT: B 266 MET cc_start: 0.7786 (ptm) cc_final: 0.6387 (ppp) REVERT: B 429 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8439 (t80) REVERT: B 482 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7211 (t70) REVERT: B 571 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6760 (m-70) REVERT: B 608 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7744 (tt) outliers start: 70 outliers final: 42 residues processed: 161 average time/residue: 0.2752 time to fit residues: 62.9099 Evaluate side-chains 145 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 571 HIS Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 571 HIS ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109793 restraints weight = 17592.070| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.66 r_work: 0.3133 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11757 Z= 0.167 Angle : 0.552 7.030 16008 Z= 0.295 Chirality : 0.042 0.162 1743 Planarity : 0.004 0.059 1922 Dihedral : 17.185 171.343 1787 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.72 % Allowed : 30.76 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1294 helix: 1.64 (0.27), residues: 377 sheet: -0.85 (0.30), residues: 309 loop : -1.88 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.016 0.001 HIS A 571 PHE 0.011 0.001 PHE B 489 TYR 0.015 0.001 TYR A 490 ARG 0.004 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.285 Fit side-chains REVERT: A 520 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5395 (pm20) REVERT: B 160 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7900 (ttmt) REVERT: B 266 MET cc_start: 0.7697 (ptm) cc_final: 0.6311 (ppp) REVERT: B 289 TYR cc_start: 0.8036 (m-80) cc_final: 0.7816 (m-10) REVERT: B 429 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7963 (t80) REVERT: B 547 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7616 (mpt180) REVERT: B 608 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7712 (tt) outliers start: 32 outliers final: 16 residues processed: 137 average time/residue: 0.2919 time to fit residues: 55.1326 Evaluate side-chains 123 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 608 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 125 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110472 restraints weight = 17538.139| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.90 r_work: 0.3157 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11757 Z= 0.171 Angle : 0.541 6.611 16008 Z= 0.287 Chirality : 0.041 0.168 1743 Planarity : 0.004 0.056 1922 Dihedral : 17.066 173.232 1787 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.99 % Allowed : 30.08 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1294 helix: 1.78 (0.27), residues: 376 sheet: -0.80 (0.30), residues: 309 loop : -1.76 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS B 107 PHE 0.011 0.001 PHE B 462 TYR 0.014 0.001 TYR A 490 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 1.325 Fit side-chains REVERT: A 520 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5340 (pm20) REVERT: B 160 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7869 (ttmt) REVERT: B 266 MET cc_start: 0.7648 (ptm) cc_final: 0.6326 (ppp) REVERT: B 289 TYR cc_start: 0.8054 (m-80) cc_final: 0.7840 (m-10) REVERT: B 403 MET cc_start: 0.8196 (tpp) cc_final: 0.7983 (tpp) REVERT: B 429 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7936 (t80) REVERT: B 488 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8278 (mtpp) REVERT: B 547 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7552 (mpt180) REVERT: B 608 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7692 (tt) outliers start: 47 outliers final: 27 residues processed: 150 average time/residue: 0.2796 time to fit residues: 58.5945 Evaluate side-chains 135 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 119 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107646 restraints weight = 17446.397| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.61 r_work: 0.3134 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11757 Z= 0.252 Angle : 0.566 6.377 16008 Z= 0.302 Chirality : 0.043 0.168 1743 Planarity : 0.004 0.059 1922 Dihedral : 17.061 172.251 1787 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.84 % Allowed : 29.14 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1294 helix: 1.83 (0.27), residues: 374 sheet: -0.80 (0.30), residues: 309 loop : -1.81 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 214 HIS 0.003 0.001 HIS B 482 PHE 0.014 0.001 PHE B 577 TYR 0.014 0.001 TYR A 490 ARG 0.005 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 105 time to evaluate : 1.275 Fit side-chains REVERT: A 137 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: A 455 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7909 (tmm160) REVERT: A 520 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5462 (pm20) REVERT: B 21 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: B 160 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7914 (ttmt) REVERT: B 266 MET cc_start: 0.7676 (ptm) cc_final: 0.6303 (ppp) REVERT: B 403 MET cc_start: 0.8166 (tpp) cc_final: 0.7932 (tpp) REVERT: B 429 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8071 (t80) REVERT: B 547 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7104 (mpt180) REVERT: B 608 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7716 (tt) outliers start: 57 outliers final: 37 residues processed: 151 average time/residue: 0.2763 time to fit residues: 58.1828 Evaluate side-chains 145 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 50 optimal weight: 0.0980 chunk 129 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109325 restraints weight = 17815.410| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.65 r_work: 0.3154 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11757 Z= 0.181 Angle : 0.543 6.934 16008 Z= 0.288 Chirality : 0.042 0.187 1743 Planarity : 0.004 0.057 1922 Dihedral : 17.009 173.032 1787 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.99 % Allowed : 29.74 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1294 helix: 1.90 (0.27), residues: 375 sheet: -0.82 (0.30), residues: 299 loop : -1.71 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.002 0.000 HIS A 571 PHE 0.012 0.001 PHE B 489 TYR 0.018 0.001 TYR B 289 ARG 0.004 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 1.298 Fit side-chains REVERT: A 520 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5471 (pm20) REVERT: B 21 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: B 160 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7857 (ttmt) REVERT: B 266 MET cc_start: 0.7550 (ptm) cc_final: 0.6197 (ppp) REVERT: B 275 MET cc_start: 0.5605 (pmm) cc_final: 0.4823 (pmm) REVERT: B 287 MET cc_start: 0.6767 (tmm) cc_final: 0.6542 (tmm) REVERT: B 403 MET cc_start: 0.8169 (tpp) cc_final: 0.7934 (tpp) REVERT: B 429 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.7976 (t80) REVERT: B 547 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7517 (mpt180) REVERT: B 608 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7668 (tt) outliers start: 47 outliers final: 35 residues processed: 142 average time/residue: 0.2915 time to fit residues: 57.5589 Evaluate side-chains 142 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 25 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105805 restraints weight = 17775.172| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.05 r_work: 0.3116 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 11757 Z= 0.340 Angle : 0.607 7.175 16008 Z= 0.322 Chirality : 0.044 0.173 1743 Planarity : 0.005 0.064 1922 Dihedral : 17.023 169.583 1787 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 5.01 % Allowed : 29.06 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1294 helix: 1.78 (0.27), residues: 374 sheet: -0.89 (0.30), residues: 299 loop : -1.83 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.004 0.001 HIS B 482 PHE 0.018 0.001 PHE B 577 TYR 0.017 0.001 TYR B 289 ARG 0.005 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 106 time to evaluate : 1.252 Fit side-chains REVERT: A 2 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7630 (ptpp) REVERT: A 520 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5443 (pm20) REVERT: B 21 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: B 76 MET cc_start: 0.5357 (tpt) cc_final: 0.3840 (ttt) REVERT: B 160 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7960 (ttmt) REVERT: B 266 MET cc_start: 0.7670 (ptm) cc_final: 0.6248 (ppp) REVERT: B 287 MET cc_start: 0.6550 (tmm) cc_final: 0.6260 (tmm) REVERT: B 403 MET cc_start: 0.8116 (tpp) cc_final: 0.7838 (tpp) REVERT: B 429 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8152 (t80) REVERT: B 488 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8330 (mtpp) REVERT: B 547 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8567 (mpt180) REVERT: B 608 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7699 (tt) outliers start: 59 outliers final: 42 residues processed: 156 average time/residue: 0.2830 time to fit residues: 61.1397 Evaluate side-chains 152 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 18 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.150249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108964 restraints weight = 17604.992| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.58 r_work: 0.3125 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11757 Z= 0.189 Angle : 0.554 8.213 16008 Z= 0.292 Chirality : 0.042 0.162 1743 Planarity : 0.004 0.058 1922 Dihedral : 17.012 170.861 1787 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.08 % Allowed : 30.08 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1294 helix: 1.91 (0.27), residues: 376 sheet: -0.80 (0.30), residues: 299 loop : -1.76 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 214 HIS 0.002 0.000 HIS B 107 PHE 0.013 0.001 PHE A 481 TYR 0.015 0.001 TYR A 490 ARG 0.008 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 1.190 Fit side-chains REVERT: A 520 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5463 (pm20) REVERT: B 21 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: B 76 MET cc_start: 0.5236 (tpt) cc_final: 0.3873 (ttt) REVERT: B 160 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7875 (ttmt) REVERT: B 266 MET cc_start: 0.7550 (ptm) cc_final: 0.6170 (ppp) REVERT: B 275 MET cc_start: 0.5550 (pmm) cc_final: 0.4812 (pmm) REVERT: B 287 MET cc_start: 0.6582 (tmm) cc_final: 0.6278 (tmm) REVERT: B 403 MET cc_start: 0.8099 (tpp) cc_final: 0.7842 (tpp) REVERT: B 429 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.7965 (t80) REVERT: B 488 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8320 (mtpp) REVERT: B 547 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7573 (mpt180) REVERT: B 608 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7673 (tt) outliers start: 48 outliers final: 38 residues processed: 148 average time/residue: 0.2881 time to fit residues: 58.7204 Evaluate side-chains 145 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 82 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 HIS B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106597 restraints weight = 17652.643| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.63 r_work: 0.3119 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11757 Z= 0.282 Angle : 0.588 8.426 16008 Z= 0.310 Chirality : 0.043 0.172 1743 Planarity : 0.004 0.062 1922 Dihedral : 16.997 169.335 1787 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 4.33 % Allowed : 30.08 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1294 helix: 1.85 (0.27), residues: 376 sheet: -0.83 (0.30), residues: 299 loop : -1.80 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 214 HIS 0.003 0.001 HIS B 482 PHE 0.015 0.001 PHE B 577 TYR 0.015 0.001 TYR B 289 ARG 0.009 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 1.243 Fit side-chains REVERT: A 520 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5456 (pm20) REVERT: B 21 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: B 76 MET cc_start: 0.5300 (tpt) cc_final: 0.3830 (ttt) REVERT: B 160 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7947 (ttmt) REVERT: B 266 MET cc_start: 0.7570 (ptm) cc_final: 0.6158 (ppp) REVERT: B 287 MET cc_start: 0.6468 (tmm) cc_final: 0.6079 (tmm) REVERT: B 403 MET cc_start: 0.8133 (tpp) cc_final: 0.7872 (tpp) REVERT: B 429 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8047 (t80) REVERT: B 488 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8333 (mtpp) REVERT: B 547 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7558 (mpt180) REVERT: B 608 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7729 (tt) outliers start: 51 outliers final: 41 residues processed: 144 average time/residue: 0.2785 time to fit residues: 55.8956 Evaluate side-chains 148 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 128 optimal weight: 0.7980 chunk 58 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0170 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 HIS ** 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 = 0.3922 r_free = 0.3922 target = 0.153038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111619 restraints weight = 17551.093| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.64 r_work: 0.3170 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11757 Z= 0.154 Angle : 0.547 9.439 16008 Z= 0.287 Chirality : 0.042 0.161 1743 Planarity : 0.004 0.054 1922 Dihedral : 16.938 172.219 1787 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.48 % Allowed : 30.59 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1294 helix: 1.99 (0.27), residues: 376 sheet: -0.68 (0.30), residues: 309 loop : -1.71 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 214 HIS 0.003 0.000 HIS B 107 PHE 0.017 0.001 PHE B 639 TYR 0.016 0.001 TYR A 490 ARG 0.009 0.000 ARG B 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.236 Fit side-chains REVERT: A 454 HIS cc_start: 0.8550 (m-70) cc_final: 0.8269 (m-70) REVERT: A 520 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5398 (pm20) REVERT: B 21 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: B 76 MET cc_start: 0.5298 (tpt) cc_final: 0.3846 (ttt) REVERT: B 160 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7823 (ttmt) REVERT: B 266 MET cc_start: 0.7427 (ptm) cc_final: 0.6114 (ppp) REVERT: B 275 MET cc_start: 0.5577 (pmm) cc_final: 0.4820 (pmm) REVERT: B 429 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 488 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8306 (mtpp) REVERT: B 547 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7557 (mpt180) REVERT: B 608 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7743 (tt) outliers start: 41 outliers final: 30 residues processed: 147 average time/residue: 0.2906 time to fit residues: 58.5183 Evaluate side-chains 137 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105006 restraints weight = 17645.437| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.04 r_work: 0.3071 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 11757 Z= 0.425 Angle : 0.662 9.793 16008 Z= 0.351 Chirality : 0.046 0.178 1743 Planarity : 0.005 0.063 1922 Dihedral : 16.998 167.532 1787 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 3.40 % Allowed : 30.76 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1294 helix: 1.72 (0.27), residues: 375 sheet: -0.81 (0.30), residues: 304 loop : -1.92 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 214 HIS 0.005 0.001 HIS B 482 PHE 0.021 0.002 PHE B 577 TYR 0.012 0.002 TYR A 714 ARG 0.008 0.000 ARG B 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5224.39 seconds wall clock time: 94 minutes 41.15 seconds (5681.15 seconds total)