Starting phenix.real_space_refine on Tue Jun 10 03:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xih_38373/06_2025/8xih_38373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xih_38373/06_2025/8xih_38373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xih_38373/06_2025/8xih_38373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xih_38373/06_2025/8xih_38373.map" model { file = "/net/cci-nas-00/data/ceres_data/8xih_38373/06_2025/8xih_38373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xih_38373/06_2025/8xih_38373.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 7326 2.51 5 N 1941 2.21 5 O 2091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11418 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4744 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 25, 'TRANS': 553} Chain breaks: 4 Chain: "B" Number of atoms: 6020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6020 Classifications: {'peptide': 735} Link IDs: {'PTRANS': 33, 'TRANS': 701} Chain breaks: 4 Chain: "G" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "H" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 337 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.96, per 1000 atoms: 0.70 Number of scatterers: 11418 At special positions: 0 Unit cell: (102, 94.35, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 31 15.00 Mg 2 11.99 O 2091 8.00 N 1941 7.00 C 7326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 33.6% alpha, 18.5% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 5.01 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: 6.78 Time building geometry restraints manager: 3.04 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1294 helix: 1.23 (0.27), residues: 372 sheet: -0.66 (0.31), residues: 295 loop : -1.95 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 214 HIS 0.004 0.001 HIS A 571 PHE 0.020 0.001 PHE A 481 TYR 0.012 0.001 TYR A 490 ARG 0.011 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.14494 ( 429) hydrogen bonds : angle 6.62370 ( 1197) covalent geometry : bond 0.00363 (11757) covalent geometry : angle 0.65521 (16008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.225 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: 0.2875 time to fit residues: 46.1284 Evaluate side-chains 109 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 580 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 66 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 568 HIS A 571 HIS B 571 HIS B 580 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104679 restraints weight = 17585.465| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.49 r_work: 0.3084 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 11757 Z= 0.340 Angle : 0.710 7.771 16008 Z= 0.379 Chirality : 0.048 0.199 1743 Planarity : 0.006 0.072 1922 Dihedral : 17.268 169.153 1792 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 5.95 % Allowed : 28.12 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1294 helix: 1.34 (0.27), residues: 380 sheet: -1.06 (0.30), residues: 314 loop : -2.07 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 131 HIS 0.008 0.001 HIS B 571 PHE 0.021 0.002 PHE B 577 TYR 0.014 0.002 TYR A 714 ARG 0.005 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.05945 ( 429) hydrogen bonds : angle 5.73875 ( 1197) covalent geometry : bond 0.00820 (11757) covalent geometry : angle 0.71001 (16008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 103 time to evaluate : 1.222 Fit side-chains REVERT: A 2 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7838 (ptpp) REVERT: A 520 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5618 (pm20) REVERT: B 266 MET cc_start: 0.7799 (ptm) cc_final: 0.6388 (ppp) REVERT: B 429 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8441 (t80) REVERT: B 482 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7211 (t70) REVERT: B 571 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6765 (m-70) REVERT: B 608 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7742 (tt) outliers start: 70 outliers final: 42 residues processed: 161 average time/residue: 0.2467 time to fit residues: 55.8742 Evaluate side-chains 145 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 571 HIS Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 571 HIS ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.150291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108904 restraints weight = 17604.585| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.62 r_work: 0.3149 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11757 Z= 0.128 Angle : 0.558 7.134 16008 Z= 0.298 Chirality : 0.042 0.202 1743 Planarity : 0.004 0.061 1922 Dihedral : 17.174 170.451 1787 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.72 % Allowed : 30.93 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1294 helix: 1.61 (0.27), residues: 377 sheet: -0.86 (0.30), residues: 309 loop : -1.90 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.012 0.001 HIS A 571 PHE 0.011 0.001 PHE B 489 TYR 0.015 0.001 TYR A 490 ARG 0.004 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 429) hydrogen bonds : angle 5.35388 ( 1197) covalent geometry : bond 0.00289 (11757) covalent geometry : angle 0.55815 (16008) *********************** 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 140 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.287 Fit side-chains REVERT: A 520 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5369 (pm20) REVERT: B 160 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7921 (ttmt) REVERT: B 266 MET cc_start: 0.7712 (ptm) cc_final: 0.6333 (ppp) REVERT: B 429 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7982 (t80) REVERT: B 547 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7610 (mpt180) REVERT: B 571 HIS cc_start: 0.6753 (OUTLIER) cc_final: 0.6523 (m-70) REVERT: B 608 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7722 (tt) outliers start: 32 outliers final: 17 residues processed: 134 average time/residue: 0.2800 time to fit residues: 51.8268 Evaluate side-chains 123 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 571 HIS Chi-restraints excluded: chain B residue 608 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 0.0770 chunk 124 optimal weight: 0.1980 chunk 116 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 125 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110537 restraints weight = 17506.050| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.64 r_work: 0.3150 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11757 Z= 0.110 Angle : 0.537 6.579 16008 Z= 0.285 Chirality : 0.042 0.202 1743 Planarity : 0.004 0.056 1922 Dihedral : 17.066 173.383 1787 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.16 % Allowed : 29.91 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1294 helix: 1.80 (0.27), residues: 376 sheet: -0.79 (0.29), residues: 319 loop : -1.76 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 214 HIS 0.004 0.000 HIS B 568 PHE 0.013 0.001 PHE B 462 TYR 0.015 0.001 TYR A 490 ARG 0.005 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 429) hydrogen bonds : angle 5.16449 ( 1197) covalent geometry : bond 0.00246 (11757) covalent geometry : angle 0.53668 (16008) *********************** 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 161 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 1.292 Fit side-chains REVERT: A 520 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5363 (pm20) REVERT: B 21 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: B 160 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7859 (ttmt) REVERT: B 266 MET cc_start: 0.7659 (ptm) cc_final: 0.6312 (ppp) REVERT: B 289 TYR cc_start: 0.8029 (m-80) cc_final: 0.7800 (m-10) REVERT: B 403 MET cc_start: 0.8186 (tpp) cc_final: 0.7976 (tpp) REVERT: B 429 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7925 (t80) REVERT: B 488 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8300 (mtpp) REVERT: B 547 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7186 (mpt180) REVERT: B 608 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7661 (tt) outliers start: 49 outliers final: 30 residues processed: 150 average time/residue: 0.2779 time to fit residues: 58.2058 Evaluate side-chains 140 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 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 650 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR 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 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 571 HIS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 119 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 447 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.148904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107259 restraints weight = 17449.241| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.63 r_work: 0.3129 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1232 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= 0.172 Angle : 0.577 6.316 16008 Z= 0.308 Chirality : 0.043 0.169 1743 Planarity : 0.004 0.060 1922 Dihedral : 17.091 171.944 1787 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.93 % Allowed : 29.23 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1294 helix: 1.84 (0.27), residues: 374 sheet: -0.81 (0.30), residues: 309 loop : -1.82 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 214 HIS 0.005 0.001 HIS B 568 PHE 0.015 0.001 PHE B 577 TYR 0.014 0.001 TYR A 490 ARG 0.006 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 429) hydrogen bonds : angle 5.19864 ( 1197) covalent geometry : bond 0.00410 (11757) covalent geometry : angle 0.57710 (16008) *********************** 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 167 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 109 time to evaluate : 1.174 Fit side-chains REVERT: A 137 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: A 455 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7908 (tmm160) REVERT: A 520 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5447 (pm20) REVERT: B 21 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: B 160 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7937 (ttmt) REVERT: B 266 MET cc_start: 0.7689 (ptm) cc_final: 0.6303 (ppp) REVERT: B 403 MET cc_start: 0.8145 (tpp) cc_final: 0.7903 (tpp) REVERT: B 429 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8102 (t80) REVERT: B 547 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7132 (mpt180) REVERT: B 608 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7729 (tt) outliers start: 58 outliers final: 35 residues processed: 155 average time/residue: 0.2598 time to fit residues: 56.1067 Evaluate side-chains 147 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 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 650 ILE Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110428 restraints weight = 17769.380| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.64 r_work: 0.3175 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1305 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= 0.113 Angle : 0.540 6.927 16008 Z= 0.286 Chirality : 0.042 0.178 1743 Planarity : 0.004 0.057 1922 Dihedral : 17.012 173.486 1787 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.08 % Allowed : 29.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1294 helix: 1.94 (0.27), residues: 375 sheet: -0.78 (0.31), residues: 299 loop : -1.70 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS A 571 PHE 0.010 0.001 PHE B 489 TYR 0.017 0.001 TYR B 289 ARG 0.005 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 429) hydrogen bonds : angle 5.05023 ( 1197) covalent geometry : bond 0.00256 (11757) covalent geometry : angle 0.54036 (16008) *********************** 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 152 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 1.275 Fit side-chains REVERT: A 520 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5459 (pm20) REVERT: B 21 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: B 76 MET cc_start: 0.5342 (tpt) cc_final: 0.3831 (ttt) REVERT: B 160 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7840 (ttmt) REVERT: B 194 VAL cc_start: 0.8062 (t) cc_final: 0.7708 (t) REVERT: B 266 MET cc_start: 0.7536 (ptm) cc_final: 0.6222 (ppp) REVERT: B 275 MET cc_start: 0.5586 (pmm) cc_final: 0.4826 (pmm) REVERT: B 403 MET cc_start: 0.8188 (tpp) cc_final: 0.7972 (tpp) REVERT: B 429 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 488 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8291 (mtpp) REVERT: B 508 LYS cc_start: 0.8342 (pptt) cc_final: 0.8057 (pttt) REVERT: B 547 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7570 (mpt180) REVERT: B 608 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7678 (tt) outliers start: 48 outliers final: 36 residues processed: 146 average time/residue: 0.2732 time to fit residues: 55.1546 Evaluate side-chains 144 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 25 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS B 445 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104996 restraints weight = 17795.277| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.50 r_work: 0.3093 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 11757 Z= 0.266 Angle : 0.656 6.863 16008 Z= 0.348 Chirality : 0.046 0.178 1743 Planarity : 0.005 0.066 1922 Dihedral : 17.099 168.931 1787 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 4.93 % Allowed : 29.48 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1294 helix: 1.70 (0.27), residues: 373 sheet: -0.89 (0.30), residues: 314 loop : -1.91 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.005 0.001 HIS A 571 PHE 0.019 0.002 PHE B 577 TYR 0.025 0.002 TYR B 289 ARG 0.007 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 429) hydrogen bonds : angle 5.32306 ( 1197) covalent geometry : bond 0.00645 (11757) covalent geometry : angle 0.65566 (16008) *********************** 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 166 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 108 time to evaluate : 1.181 Fit side-chains REVERT: A 2 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7703 (ptpp) REVERT: A 520 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5453 (pm20) REVERT: B 21 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: B 76 MET cc_start: 0.5101 (tpt) cc_final: 0.3738 (ttt) REVERT: B 160 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8016 (ttmt) REVERT: B 266 MET cc_start: 0.7720 (ptm) cc_final: 0.6282 (ppp) REVERT: B 403 MET cc_start: 0.8122 (tpp) cc_final: 0.7845 (tpp) REVERT: B 429 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8307 (t80) REVERT: B 488 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8336 (mtpp) REVERT: B 547 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8582 (mpt180) REVERT: B 608 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7752 (tt) outliers start: 58 outliers final: 42 residues processed: 157 average time/residue: 0.2633 time to fit residues: 57.3946 Evaluate side-chains 152 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 161 LEU 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 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 650 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 18 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107506 restraints weight = 17670.798| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.12 r_work: 0.3138 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11757 Z= 0.150 Angle : 0.578 7.975 16008 Z= 0.306 Chirality : 0.043 0.164 1743 Planarity : 0.004 0.062 1922 Dihedral : 17.091 168.462 1787 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.25 % Allowed : 30.25 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1294 helix: 1.77 (0.27), residues: 377 sheet: -0.72 (0.30), residues: 304 loop : -1.86 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 214 HIS 0.003 0.001 HIS B 482 PHE 0.013 0.001 PHE B 577 TYR 0.019 0.001 TYR B 289 ARG 0.007 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 429) hydrogen bonds : angle 5.17447 ( 1197) covalent geometry : bond 0.00355 (11757) covalent geometry : angle 0.57809 (16008) *********************** 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 156 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 1.307 Fit side-chains REVERT: A 2 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7632 (ptpp) REVERT: A 520 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5429 (pm20) REVERT: A 530 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7652 (mtm110) REVERT: B 21 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: B 76 MET cc_start: 0.5169 (tpt) cc_final: 0.3721 (ttt) REVERT: B 160 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7938 (ttmt) REVERT: B 194 VAL cc_start: 0.8049 (t) cc_final: 0.7724 (t) REVERT: B 266 MET cc_start: 0.7676 (ptm) cc_final: 0.6263 (ppp) REVERT: B 403 MET cc_start: 0.8115 (tpp) cc_final: 0.7850 (tpp) REVERT: B 429 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8036 (t80) REVERT: B 547 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8505 (mpt180) REVERT: B 608 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7748 (tt) outliers start: 50 outliers final: 39 residues processed: 147 average time/residue: 0.2796 time to fit residues: 55.9584 Evaluate side-chains 151 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 161 LEU 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 591 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS 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 82 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 27 optimal weight: 0.0570 chunk 78 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 HIS B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109453 restraints weight = 17564.803| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.61 r_work: 0.3136 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1401 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= 0.122 Angle : 0.558 8.565 16008 Z= 0.293 Chirality : 0.042 0.165 1743 Planarity : 0.004 0.058 1922 Dihedral : 17.008 170.246 1787 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.74 % Allowed : 30.84 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1294 helix: 1.87 (0.27), residues: 378 sheet: -0.78 (0.30), residues: 299 loop : -1.74 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 214 HIS 0.003 0.000 HIS B 107 PHE 0.014 0.001 PHE B 639 TYR 0.019 0.001 TYR B 289 ARG 0.008 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 429) hydrogen bonds : angle 5.02450 ( 1197) covalent geometry : bond 0.00281 (11757) covalent geometry : angle 0.55776 (16008) *********************** 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 153 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.305 Fit side-chains REVERT: A 520 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5414 (pm20) REVERT: A 530 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7635 (mtm110) REVERT: A 570 ARG cc_start: 0.8075 (tpp-160) cc_final: 0.7831 (tpm170) REVERT: B 21 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: B 76 MET cc_start: 0.5216 (tpt) cc_final: 0.3811 (ttt) REVERT: B 160 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7872 (ttmt) REVERT: B 266 MET cc_start: 0.7542 (ptm) cc_final: 0.6175 (ppp) REVERT: B 429 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.7892 (t80) REVERT: B 484 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9056 (tt) REVERT: B 547 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7578 (mpt180) REVERT: B 608 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7683 (tt) outliers start: 44 outliers final: 37 residues processed: 146 average time/residue: 0.2739 time to fit residues: 55.3540 Evaluate side-chains 149 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 161 LEU 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 591 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 128 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111312 restraints weight = 17562.715| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.65 r_work: 0.3162 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11757 Z= 0.111 Angle : 0.557 9.802 16008 Z= 0.291 Chirality : 0.042 0.162 1743 Planarity : 0.004 0.056 1922 Dihedral : 16.928 172.070 1787 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.40 % Allowed : 30.93 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1294 helix: 2.00 (0.27), residues: 378 sheet: -0.73 (0.30), residues: 314 loop : -1.76 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 214 HIS 0.003 0.000 HIS B 107 PHE 0.017 0.001 PHE A 481 TYR 0.015 0.001 TYR A 490 ARG 0.008 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 429) hydrogen bonds : angle 4.93368 ( 1197) covalent geometry : bond 0.00252 (11757) covalent geometry : angle 0.55665 (16008) ********************** 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 153 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.307 Fit side-chains REVERT: A 520 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5427 (pm20) REVERT: A 530 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7628 (mtm110) REVERT: B 21 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: B 76 MET cc_start: 0.5237 (tpt) cc_final: 0.3818 (ttt) REVERT: B 160 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7832 (ttmt) REVERT: B 194 VAL cc_start: 0.7828 (t) cc_final: 0.7588 (t) REVERT: B 266 MET cc_start: 0.7432 (ptm) cc_final: 0.6139 (ppp) REVERT: B 275 MET cc_start: 0.5593 (pmm) cc_final: 0.4830 (pmm) REVERT: B 287 MET cc_start: 0.6385 (tmm) cc_final: 0.6075 (tmm) REVERT: B 429 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 508 LYS cc_start: 0.8304 (pptt) cc_final: 0.7949 (pttt) REVERT: B 547 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7632 (mpt180) REVERT: B 608 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7685 (tt) outliers start: 40 outliers final: 32 residues processed: 147 average time/residue: 0.3203 time to fit residues: 64.5929 Evaluate side-chains 141 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 161 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 591 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106280 restraints weight = 17531.620| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.62 r_work: 0.3110 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 11757 Z= 0.221 Angle : 0.632 9.785 16008 Z= 0.334 Chirality : 0.045 0.339 1743 Planarity : 0.005 0.063 1922 Dihedral : 17.001 167.662 1787 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.99 % Allowed : 30.59 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1294 helix: 1.83 (0.27), residues: 377 sheet: -0.84 (0.29), residues: 319 loop : -1.87 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 214 HIS 0.004 0.001 HIS B 568 PHE 0.018 0.001 PHE B 577 TYR 0.014 0.002 TYR B 434 ARG 0.009 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 429) hydrogen bonds : angle 5.15210 ( 1197) covalent geometry : bond 0.00534 (11757) covalent geometry : angle 0.63169 (16008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5794.41 seconds wall clock time: 101 minutes 35.71 seconds (6095.71 seconds total)