Starting phenix.real_space_refine on Sat Aug 23 09:44:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xih_38373/08_2025/8xih_38373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xih_38373/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2025/8xih_38373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2025/8xih_38373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2025/8xih_38373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2025/8xih_38373.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.68, per 1000 atoms: 0.23 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: 0.75 Conformation dependent library (CDL) restraints added in 559.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.06 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: 1.73 Time building geometry restraints manager: 1.03 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.840 ------------------------------------------------------------------------------- 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= 0.161 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.000 ARG B 128 TYR 0.012 0.001 TYR A 490 PHE 0.020 0.001 PHE A 481 TRP 0.017 0.001 TRP A 214 HIS 0.004 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00363 (11757) covalent geometry : angle 0.65521 (16008) hydrogen bonds : bond 0.14494 ( 429) hydrogen bonds : angle 6.62370 ( 1197) *********************** 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 : 0.454 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: 0.1037 time to fit residues: 16.7670 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 : 0.334 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS B 571 HIS B 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111026 restraints weight = 17492.027| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.62 r_work: 0.3151 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11757 Z= 0.137 Angle : 0.551 7.134 16008 Z= 0.293 Chirality : 0.042 0.198 1743 Planarity : 0.005 0.062 1922 Dihedral : 17.292 175.510 1792 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.06 % Allowed : 29.48 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.24), residues: 1294 helix: 1.72 (0.28), residues: 374 sheet: -0.84 (0.31), residues: 299 loop : -1.80 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.014 0.001 TYR A 490 PHE 0.014 0.001 PHE B 577 TRP 0.008 0.001 TRP A 131 HIS 0.007 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00314 (11757) covalent geometry : angle 0.55072 (16008) hydrogen bonds : bond 0.04023 ( 429) hydrogen bonds : angle 5.39043 ( 1197) *********************** 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 146 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.426 Fit side-chains REVERT: B 160 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (ttmt) REVERT: B 266 MET cc_start: 0.7713 (ptm) cc_final: 0.6404 (ppp) REVERT: B 488 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8293 (mtpp) REVERT: B 608 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7665 (tt) outliers start: 36 outliers final: 18 residues processed: 138 average time/residue: 0.1164 time to fit residues: 22.4423 Evaluate side-chains 124 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 659 VAL 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 160 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 571 HIS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111805 restraints weight = 17630.796| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.62 r_work: 0.3166 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11757 Z= 0.113 Angle : 0.530 6.530 16008 Z= 0.281 Chirality : 0.042 0.195 1743 Planarity : 0.004 0.056 1922 Dihedral : 17.161 176.747 1787 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.06 % Allowed : 29.40 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.24), residues: 1294 helix: 1.82 (0.28), residues: 376 sheet: -0.79 (0.31), residues: 298 loop : -1.71 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.014 0.001 TYR A 490 PHE 0.010 0.001 PHE B 577 TRP 0.008 0.001 TRP A 214 HIS 0.004 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00253 (11757) covalent geometry : angle 0.52997 (16008) hydrogen bonds : bond 0.03470 ( 429) hydrogen bonds : angle 5.14800 ( 1197) *********************** 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 149 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.334 Fit side-chains REVERT: A 520 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5447 (pm20) REVERT: B 21 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: B 160 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7828 (ttmt) REVERT: B 266 MET cc_start: 0.7560 (ptm) cc_final: 0.6315 (ppp) REVERT: B 429 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8043 (t80) REVERT: B 608 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7682 (tt) outliers start: 36 outliers final: 19 residues processed: 142 average time/residue: 0.1140 time to fit residues: 22.4571 Evaluate side-chains 127 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 TYR 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 659 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR 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 160 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 671 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112473 restraints weight = 17615.791| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.59 r_work: 0.3170 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11757 Z= 0.112 Angle : 0.528 6.342 16008 Z= 0.278 Chirality : 0.041 0.197 1743 Planarity : 0.004 0.054 1922 Dihedral : 17.110 177.239 1787 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.48 % Allowed : 29.14 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.24), residues: 1294 helix: 1.93 (0.27), residues: 375 sheet: -0.78 (0.31), residues: 298 loop : -1.68 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.014 0.001 TYR A 490 PHE 0.011 0.001 PHE B 577 TRP 0.009 0.001 TRP A 214 HIS 0.002 0.000 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00254 (11757) covalent geometry : angle 0.52770 (16008) hydrogen bonds : bond 0.03287 ( 429) hydrogen bonds : angle 5.03745 ( 1197) *********************** 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 147 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.478 Fit side-chains REVERT: A 455 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7903 (tmm160) REVERT: A 520 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5421 (pm20) REVERT: B 21 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: B 160 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7795 (ttmt) REVERT: B 266 MET cc_start: 0.7539 (ptm) cc_final: 0.6325 (ppp) REVERT: B 289 TYR cc_start: 0.7999 (m-80) cc_final: 0.7777 (m-10) REVERT: B 429 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8026 (t80) REVERT: B 488 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8263 (mtpp) REVERT: B 608 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7638 (tt) outliers start: 41 outliers final: 26 residues processed: 141 average time/residue: 0.1128 time to fit residues: 22.2924 Evaluate side-chains 132 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE 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 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 571 HIS Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR 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 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 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 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 = 0.3862 r_free = 0.3862 target = 0.147895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106808 restraints weight = 17641.687| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.53 r_work: 0.3111 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 11757 Z= 0.220 Angle : 0.612 6.776 16008 Z= 0.326 Chirality : 0.044 0.172 1743 Planarity : 0.005 0.063 1922 Dihedral : 17.111 172.913 1786 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 5.18 % Allowed : 28.12 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.24), residues: 1294 helix: 1.81 (0.27), residues: 374 sheet: -0.85 (0.30), residues: 308 loop : -1.81 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 128 TYR 0.012 0.001 TYR A 490 PHE 0.016 0.001 PHE B 577 TRP 0.009 0.002 TRP A 214 HIS 0.013 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00527 (11757) covalent geometry : angle 0.61190 (16008) hydrogen bonds : bond 0.04663 ( 429) hydrogen bonds : angle 5.22947 ( 1197) *********************** 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 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7698 (ptpp) REVERT: A 520 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5438 (pm20) REVERT: B 21 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: B 160 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7986 (ttmt) REVERT: B 266 MET cc_start: 0.7654 (ptm) cc_final: 0.6286 (ppp) REVERT: B 429 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8281 (t80) REVERT: B 482 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.6940 (t70) REVERT: B 488 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8290 (mtpp) REVERT: B 608 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7758 (tt) outliers start: 61 outliers final: 39 residues processed: 157 average time/residue: 0.1060 time to fit residues: 23.2149 Evaluate side-chains 146 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 522 ARG 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 701 LEU 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 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 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 172 THR 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 396 LEU 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 482 HIS Chi-restraints excluded: chain B residue 523 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 382 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS B 290 ASN B 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105028 restraints weight = 17920.805| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.66 r_work: 0.3092 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 11757 Z= 0.241 Angle : 0.631 7.150 16008 Z= 0.336 Chirality : 0.046 0.217 1743 Planarity : 0.005 0.067 1922 Dihedral : 17.180 168.038 1786 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 5.69 % Allowed : 27.70 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.23), residues: 1294 helix: 1.67 (0.27), residues: 373 sheet: -0.88 (0.30), residues: 313 loop : -1.89 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.023 0.002 TYR B 289 PHE 0.018 0.001 PHE B 577 TRP 0.014 0.002 TRP A 214 HIS 0.004 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00579 (11757) covalent geometry : angle 0.63143 (16008) hydrogen bonds : bond 0.04838 ( 429) hydrogen bonds : angle 5.32371 ( 1197) *********************** 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 171 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 104 time to evaluate : 0.445 Fit side-chains REVERT: A 2 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7699 (ptpp) REVERT: A 137 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7854 (mm-40) REVERT: A 520 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5523 (pm20) REVERT: B 76 MET cc_start: 0.5193 (tpt) cc_final: 0.3703 (ttt) REVERT: B 160 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (ttmt) REVERT: B 266 MET cc_start: 0.7777 (ptm) cc_final: 0.6382 (ppp) REVERT: B 287 MET cc_start: 0.6613 (tmm) cc_final: 0.6364 (tmm) REVERT: B 429 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8283 (t80) REVERT: B 482 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7049 (t70) REVERT: B 488 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8351 (mtpp) REVERT: B 547 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7242 (mpt180) REVERT: B 608 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7751 (tt) outliers start: 67 outliers final: 42 residues processed: 159 average time/residue: 0.1148 time to fit residues: 25.3898 Evaluate side-chains 150 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 137 GLN 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 318 ILE 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 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 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP 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 396 LEU 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 482 HIS 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 721 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106184 restraints weight = 17666.140| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.08 r_work: 0.3117 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11757 Z= 0.197 Angle : 0.604 7.522 16008 Z= 0.322 Chirality : 0.044 0.197 1743 Planarity : 0.005 0.066 1922 Dihedral : 17.147 166.857 1786 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 5.10 % Allowed : 29.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.23), residues: 1294 helix: 1.68 (0.27), residues: 375 sheet: -0.80 (0.30), residues: 303 loop : -1.85 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 128 TYR 0.019 0.001 TYR B 289 PHE 0.016 0.001 PHE B 577 TRP 0.018 0.002 TRP A 214 HIS 0.004 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00472 (11757) covalent geometry : angle 0.60442 (16008) hydrogen bonds : bond 0.04414 ( 429) hydrogen bonds : angle 5.25832 ( 1197) *********************** 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 168 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 108 time to evaluate : 0.450 Fit side-chains REVERT: A 2 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7625 (ptpp) REVERT: A 137 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7802 (mm-40) REVERT: A 520 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: B 21 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: B 76 MET cc_start: 0.5177 (tpt) cc_final: 0.3743 (ttt) REVERT: B 160 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7938 (ttmt) REVERT: B 266 MET cc_start: 0.7732 (ptm) cc_final: 0.6319 (ppp) REVERT: B 287 MET cc_start: 0.6492 (tmm) cc_final: 0.6178 (tmm) REVERT: B 429 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 547 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7325 (mpt180) REVERT: B 608 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 637 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7766 (ttp80) outliers start: 60 outliers final: 42 residues processed: 158 average time/residue: 0.1175 time to fit residues: 25.6043 Evaluate side-chains 153 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 137 GLN 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 318 ILE 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 608 LEU 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 689 ASP 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 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 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 392 VAL Chi-restraints excluded: chain B residue 396 LEU 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 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 721 THR 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 101 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 68 optimal weight: 8.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 571 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 = 0.3859 r_free = 0.3859 target = 0.147807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107296 restraints weight = 17608.189| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.42 r_work: 0.3128 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11757 Z= 0.181 Angle : 0.595 9.149 16008 Z= 0.316 Chirality : 0.044 0.185 1743 Planarity : 0.005 0.065 1922 Dihedral : 17.111 166.435 1786 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 5.18 % Allowed : 29.06 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.23), residues: 1294 helix: 1.73 (0.27), residues: 375 sheet: -0.79 (0.30), residues: 303 loop : -1.85 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 128 TYR 0.018 0.001 TYR B 289 PHE 0.015 0.001 PHE B 577 TRP 0.022 0.002 TRP A 214 HIS 0.003 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00432 (11757) covalent geometry : angle 0.59509 (16008) hydrogen bonds : bond 0.04260 ( 429) hydrogen bonds : angle 5.21530 ( 1197) *********************** 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 170 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 109 time to evaluate : 0.288 Fit side-chains REVERT: A 2 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7622 (ptpp) REVERT: A 137 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7815 (mm-40) REVERT: A 520 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5368 (pm20) REVERT: B 21 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 76 MET cc_start: 0.4982 (tpt) cc_final: 0.3663 (ttt) REVERT: B 160 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7936 (ttmt) REVERT: B 266 MET cc_start: 0.7689 (ptm) cc_final: 0.6311 (ppp) REVERT: B 429 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8263 (t80) REVERT: B 488 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8192 (mmmt) REVERT: B 547 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7291 (mpt180) REVERT: B 608 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7740 (tt) REVERT: B 637 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7647 (ttp80) outliers start: 61 outliers final: 44 residues processed: 158 average time/residue: 0.1136 time to fit residues: 24.5095 Evaluate side-chains 157 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 137 GLN 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 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 571 HIS Chi-restraints excluded: chain A residue 591 VAL 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 689 ASP 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 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 392 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 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 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 721 THR Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 454 HIS A 571 HIS B 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109313 restraints weight = 17421.338| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.54 r_work: 0.3137 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1428 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= 0.119 Angle : 0.570 10.143 16008 Z= 0.301 Chirality : 0.042 0.186 1743 Planarity : 0.004 0.061 1922 Dihedral : 17.083 167.086 1786 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.48 % Allowed : 30.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1294 helix: 1.87 (0.27), residues: 377 sheet: -0.70 (0.30), residues: 303 loop : -1.79 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 128 TYR 0.015 0.001 TYR A 490 PHE 0.015 0.001 PHE A 481 TRP 0.022 0.001 TRP A 214 HIS 0.004 0.000 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00271 (11757) covalent geometry : angle 0.57039 (16008) hydrogen bonds : bond 0.03492 ( 429) hydrogen bonds : angle 5.09136 ( 1197) *********************** 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 145 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.444 Fit side-chains REVERT: A 520 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5393 (pm20) REVERT: B 21 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: B 76 MET cc_start: 0.5151 (tpt) cc_final: 0.3765 (ttt) REVERT: B 160 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7857 (ttmt) REVERT: B 266 MET cc_start: 0.7568 (ptm) cc_final: 0.6157 (ppp) REVERT: B 287 MET cc_start: 0.6684 (tmm) cc_final: 0.6470 (tmm) REVERT: B 429 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 547 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7197 (mpt180) REVERT: B 608 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7713 (tt) outliers start: 41 outliers final: 32 residues processed: 137 average time/residue: 0.1233 time to fit residues: 23.4169 Evaluate side-chains 138 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 571 HIS 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108025 restraints weight = 17716.791| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.40 r_work: 0.3106 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11757 Z= 0.178 Angle : 0.606 10.561 16008 Z= 0.320 Chirality : 0.043 0.182 1743 Planarity : 0.005 0.063 1922 Dihedral : 17.064 166.194 1786 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 3.82 % Allowed : 30.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.24), residues: 1294 helix: 1.82 (0.27), residues: 377 sheet: -0.75 (0.30), residues: 308 loop : -1.83 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 128 TYR 0.014 0.001 TYR A 490 PHE 0.015 0.001 PHE B 577 TRP 0.022 0.002 TRP A 214 HIS 0.006 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00426 (11757) covalent geometry : angle 0.60564 (16008) hydrogen bonds : bond 0.04092 ( 429) hydrogen bonds : angle 5.12364 ( 1197) ********************** 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 149 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 0.459 Fit side-chains REVERT: A 520 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5363 (pm20) REVERT: B 21 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: B 76 MET cc_start: 0.5208 (tpt) cc_final: 0.3792 (ttt) REVERT: B 160 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7936 (ttmt) REVERT: B 266 MET cc_start: 0.7587 (ptm) cc_final: 0.6164 (ppp) REVERT: B 287 MET cc_start: 0.6644 (tmm) cc_final: 0.6409 (tmm) REVERT: B 429 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 547 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7269 (mpt180) REVERT: B 608 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7723 (tt) REVERT: B 637 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7633 (ttp80) outliers start: 45 outliers final: 37 residues processed: 141 average time/residue: 0.1213 time to fit residues: 23.6088 Evaluate side-chains 147 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain A residue 366 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 591 VAL Chi-restraints excluded: chain A residue 608 LEU 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 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 392 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 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 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 99 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 0.0770 chunk 47 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 112 optimal weight: 0.0030 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.4948 ------------------------------------------------------------------------------- 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** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112030 restraints weight = 17600.994| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.62 r_work: 0.3177 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1545 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= 0.110 Angle : 0.560 10.345 16008 Z= 0.294 Chirality : 0.042 0.179 1743 Planarity : 0.004 0.056 1922 Dihedral : 16.966 170.103 1786 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.55 % Allowed : 31.27 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.24), residues: 1294 helix: 1.98 (0.27), residues: 378 sheet: -0.72 (0.30), residues: 322 loop : -1.73 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 128 TYR 0.016 0.001 TYR A 490 PHE 0.011 0.001 PHE B 489 TRP 0.017 0.001 TRP A 214 HIS 0.003 0.000 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00248 (11757) covalent geometry : angle 0.56016 (16008) hydrogen bonds : bond 0.02995 ( 429) hydrogen bonds : angle 4.95348 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.27 seconds wall clock time: 40 minutes 38.59 seconds (2438.59 seconds total)