Starting phenix.real_space_refine on Sun Dec 29 19:36:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xih_38373/12_2024/8xih_38373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xih_38373/12_2024/8xih_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_38373/12_2024/8xih_38373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xih_38373/12_2024/8xih_38373.map" model { file = "/net/cci-nas-00/data/ceres_data/8xih_38373/12_2024/8xih_38373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xih_38373/12_2024/8xih_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.02, per 1000 atoms: 0.61 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: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 33.6% alpha, 18.5% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.96 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: 4.06 Time building geometry restraints manager: 3.37 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: 0.750 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 30.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11757 Z= 0.232 Angle : 0.655 11.026 16008 Z= 0.346 Chirality : 0.046 0.276 1743 Planarity : 0.005 0.085 1922 Dihedral : 20.099 179.842 4467 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.93 % Allowed : 31.18 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1294 helix: 1.23 (0.27), residues: 372 sheet: -0.66 (0.31), residues: 295 loop : -1.95 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 214 HIS 0.004 0.001 HIS A 571 PHE 0.020 0.001 PHE A 481 TYR 0.012 0.001 TYR A 490 ARG 0.011 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.355 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: 0.2893 time to fit residues: 46.6155 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 : 1.317 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 11757 Z= 0.536 Angle : 0.710 7.771 16008 Z= 0.379 Chirality : 0.048 0.199 1743 Planarity : 0.006 0.072 1922 Dihedral : 17.268 169.153 1792 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 5.95 % Allowed : 28.12 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1294 helix: 1.34 (0.27), residues: 380 sheet: -1.06 (0.30), residues: 314 loop : -2.07 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 131 HIS 0.008 0.001 HIS B 571 PHE 0.021 0.002 PHE B 577 TYR 0.014 0.002 TYR A 714 ARG 0.005 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 103 time to evaluate : 1.249 Fit side-chains REVERT: A 2 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7995 (ptpp) REVERT: A 520 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5515 (pm20) REVERT: B 84 ILE cc_start: -0.2367 (OUTLIER) cc_final: -0.2569 (tt) REVERT: B 266 MET cc_start: 0.7650 (ptm) cc_final: 0.6453 (ppp) REVERT: B 429 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8418 (t80) REVERT: B 482 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6286 (t70) REVERT: B 571 HIS cc_start: 0.7083 (OUTLIER) cc_final: 0.6775 (m-70) REVERT: B 608 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7694 (tt) outliers start: 70 outliers final: 42 residues processed: 161 average time/residue: 0.2746 time to fit residues: 62.7357 Evaluate side-chains 146 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 97 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 84 ILE 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 66 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 11757 Z= 0.344 Angle : 0.622 7.540 16008 Z= 0.333 Chirality : 0.045 0.208 1743 Planarity : 0.005 0.070 1922 Dihedral : 17.186 167.955 1787 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 5.27 % Allowed : 29.23 % 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: -1.07 (0.23), residues: 1294 helix: 1.43 (0.27), residues: 375 sheet: -0.94 (0.30), residues: 303 loop : -2.00 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 214 HIS 0.008 0.001 HIS A 571 PHE 0.013 0.001 PHE B 577 TYR 0.013 0.001 TYR A 490 ARG 0.004 0.000 ARG A 530 *********************** 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 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 107 time to evaluate : 1.194 Fit side-chains REVERT: A 2 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7893 (ptpp) REVERT: A 137 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7978 (mm-40) REVERT: A 520 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5430 (pm20) REVERT: B 160 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8045 (ttmt) REVERT: B 266 MET cc_start: 0.7608 (ptm) cc_final: 0.6387 (ppp) REVERT: B 429 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8196 (t80) REVERT: B 547 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8571 (mpt180) REVERT: B 608 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7714 (tt) outliers start: 62 outliers final: 37 residues processed: 158 average time/residue: 0.2818 time to fit residues: 61.5634 Evaluate side-chains 143 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 159 TYR 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 580 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 703 SER 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 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 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 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 519 VAL 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 590 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 628 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11757 Z= 0.258 Angle : 0.581 6.398 16008 Z= 0.311 Chirality : 0.043 0.204 1743 Planarity : 0.005 0.067 1922 Dihedral : 17.133 167.852 1787 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.86 % Allowed : 28.80 % Favored : 65.34 % 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: -0.95 (0.23), residues: 1294 helix: 1.58 (0.27), residues: 375 sheet: -0.92 (0.30), residues: 309 loop : -1.93 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 131 HIS 0.003 0.001 HIS B 482 PHE 0.015 0.001 PHE B 462 TYR 0.014 0.001 TYR A 490 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 108 time to evaluate : 1.316 Fit side-chains REVERT: A 2 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7794 (ptpp) REVERT: A 137 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7974 (mm-40) REVERT: A 520 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5316 (pm20) REVERT: B 160 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: B 266 MET cc_start: 0.7571 (ptm) cc_final: 0.6348 (ppp) REVERT: B 289 TYR cc_start: 0.8077 (m-80) cc_final: 0.7728 (m-10) REVERT: B 429 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 547 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8493 (mpt180) REVERT: B 571 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6485 (m90) REVERT: B 608 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7687 (tt) outliers start: 69 outliers final: 46 residues processed: 166 average time/residue: 0.2799 time to fit residues: 64.2672 Evaluate side-chains 159 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 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 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 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 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 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 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 470 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 519 VAL 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 Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 641 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 454 HIS B 445 GLN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11757 Z= 0.302 Angle : 0.597 6.443 16008 Z= 0.319 Chirality : 0.044 0.170 1743 Planarity : 0.005 0.068 1922 Dihedral : 17.120 171.278 1787 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 6.37 % Allowed : 28.21 % 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: -0.97 (0.23), residues: 1294 helix: 1.57 (0.27), residues: 375 sheet: -0.93 (0.30), residues: 304 loop : -1.95 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 214 HIS 0.004 0.001 HIS B 571 PHE 0.014 0.001 PHE B 577 TYR 0.014 0.001 TYR A 490 ARG 0.004 0.000 ARG A 456 *********************** 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 184 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 109 time to evaluate : 1.405 Fit side-chains REVERT: A 2 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7790 (ptpp) REVERT: A 137 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8004 (mm-40) REVERT: A 455 ARG cc_start: 0.8064 (ttp-170) cc_final: 0.7839 (tmm160) REVERT: A 520 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5307 (pm20) REVERT: B 160 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8030 (ttmt) REVERT: B 289 TYR cc_start: 0.8023 (m-80) cc_final: 0.7803 (m-10) REVERT: B 429 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 547 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8503 (mpt180) REVERT: B 571 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6538 (m-70) REVERT: B 608 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7703 (tt) outliers start: 75 outliers final: 59 residues processed: 174 average time/residue: 0.2763 time to fit residues: 68.2925 Evaluate side-chains 168 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 101 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 689 ASP 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 757 SER 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 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 LEU 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 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 470 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 519 VAL 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 571 HIS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 628 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.0370 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 11757 Z= 0.154 Angle : 0.543 6.846 16008 Z= 0.290 Chirality : 0.041 0.159 1743 Planarity : 0.004 0.059 1922 Dihedral : 17.033 167.956 1787 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.91 % Allowed : 30.59 % 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: -0.72 (0.24), residues: 1294 helix: 1.81 (0.27), residues: 376 sheet: -0.86 (0.30), residues: 299 loop : -1.78 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.010 0.001 HIS B 571 PHE 0.011 0.001 PHE B 489 TYR 0.016 0.001 TYR A 490 ARG 0.005 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 1.359 Fit side-chains REVERT: A 455 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7789 (tmm160) REVERT: A 520 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5247 (pm20) REVERT: B 21 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: B 160 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7916 (ttmt) REVERT: B 194 VAL cc_start: 0.7900 (t) cc_final: 0.7631 (t) REVERT: B 266 MET cc_start: 0.7477 (ptm) cc_final: 0.6350 (ppp) REVERT: B 275 MET cc_start: 0.5605 (pmm) cc_final: 0.4816 (pmm) REVERT: B 289 TYR cc_start: 0.7983 (m-80) cc_final: 0.7719 (m-10) REVERT: B 429 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.7968 (t80) REVERT: B 547 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7545 (mpt180) REVERT: B 608 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7610 (tt) outliers start: 46 outliers final: 28 residues processed: 150 average time/residue: 0.2937 time to fit residues: 61.3191 Evaluate side-chains 142 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 312 GLU 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 650 ILE 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 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 164 LEU Chi-restraints excluded: chain B residue 172 THR 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 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 671 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11757 Z= 0.206 Angle : 0.560 8.255 16008 Z= 0.296 Chirality : 0.042 0.166 1743 Planarity : 0.004 0.058 1922 Dihedral : 16.993 168.200 1787 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.42 % Allowed : 29.99 % 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: -0.72 (0.23), residues: 1294 helix: 1.81 (0.27), residues: 377 sheet: -0.85 (0.30), residues: 299 loop : -1.80 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 214 HIS 0.003 0.001 HIS B 571 PHE 0.012 0.001 PHE B 577 TYR 0.015 0.001 TYR A 490 ARG 0.007 0.000 ARG B 195 *********************** 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 159 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 1.305 Fit side-chains REVERT: A 152 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7565 (m-40) REVERT: A 520 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5253 (pm20) REVERT: B 21 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: B 160 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7955 (ttmt) REVERT: B 266 MET cc_start: 0.7470 (ptm) cc_final: 0.6317 (ppp) REVERT: B 289 TYR cc_start: 0.7999 (m-80) cc_final: 0.7696 (m-10) REVERT: B 429 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7965 (t80) REVERT: B 546 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8526 (t0) REVERT: B 547 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8455 (mpt180) REVERT: B 571 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6545 (m90) REVERT: B 608 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7623 (tt) outliers start: 52 outliers final: 35 residues processed: 150 average time/residue: 0.2765 time to fit residues: 57.8681 Evaluate side-chains 147 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 152 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 438 SER 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 687 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 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 571 HIS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 671 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11757 Z= 0.242 Angle : 0.577 8.355 16008 Z= 0.304 Chirality : 0.043 0.168 1743 Planarity : 0.004 0.060 1922 Dihedral : 16.997 167.489 1787 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.67 % Allowed : 29.74 % 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: -0.74 (0.23), residues: 1294 helix: 1.81 (0.27), residues: 377 sheet: -0.84 (0.30), residues: 299 loop : -1.83 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 214 HIS 0.003 0.001 HIS B 482 PHE 0.013 0.001 PHE B 577 TYR 0.014 0.001 TYR A 490 ARG 0.007 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 1.311 Fit side-chains REVERT: A 152 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7582 (m-40) REVERT: A 520 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5276 (pm20) REVERT: B 21 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: B 160 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7982 (ttmt) REVERT: B 266 MET cc_start: 0.7484 (ptm) cc_final: 0.6300 (ppp) REVERT: B 289 TYR cc_start: 0.7970 (m-80) cc_final: 0.7606 (m-10) REVERT: B 429 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8001 (t80) REVERT: B 547 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7144 (mpt180) REVERT: B 571 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6434 (m90) REVERT: B 608 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7640 (tt) outliers start: 55 outliers final: 43 residues processed: 150 average time/residue: 0.2720 time to fit residues: 57.7110 Evaluate side-chains 152 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 152 ASN 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 438 SER 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 650 ILE 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 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 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 264 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 0.0030 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 546 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1426 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= 0.161 Angle : 0.560 10.020 16008 Z= 0.294 Chirality : 0.042 0.163 1743 Planarity : 0.004 0.058 1922 Dihedral : 16.960 168.587 1787 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.08 % Allowed : 30.42 % 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: -0.66 (0.24), residues: 1294 helix: 1.87 (0.27), residues: 378 sheet: -0.80 (0.30), residues: 309 loop : -1.79 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 214 HIS 0.003 0.000 HIS B 571 PHE 0.012 0.001 PHE B 489 TYR 0.028 0.001 TYR B 521 ARG 0.008 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 1.255 Fit side-chains REVERT: A 152 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7548 (m-40) REVERT: A 520 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5275 (pm20) REVERT: B 21 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6610 (m-80) REVERT: B 160 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7888 (ttmt) REVERT: B 194 VAL cc_start: 0.7925 (t) cc_final: 0.7652 (t) REVERT: B 266 MET cc_start: 0.7395 (ptm) cc_final: 0.6240 (ppp) REVERT: B 289 TYR cc_start: 0.8049 (m-80) cc_final: 0.7729 (m-10) REVERT: B 403 MET cc_start: 0.8083 (tpp) cc_final: 0.7862 (tpp) REVERT: B 429 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7776 (t80) REVERT: B 508 LYS cc_start: 0.8416 (pptt) cc_final: 0.8125 (pttt) REVERT: B 546 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8543 (t0) REVERT: B 547 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8437 (mpt180) REVERT: B 608 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7613 (tt) outliers start: 48 outliers final: 34 residues processed: 147 average time/residue: 0.2712 time to fit residues: 57.3224 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 : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 152 ASN 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 312 GLU 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 438 SER 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 721 THR 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 81 ILE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 40.0000 chunk 82 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 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 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 11757 Z= 0.418 Angle : 0.672 9.359 16008 Z= 0.355 Chirality : 0.046 0.193 1743 Planarity : 0.005 0.066 1922 Dihedral : 17.045 167.968 1787 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 3.99 % Allowed : 30.42 % 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: -0.96 (0.23), residues: 1294 helix: 1.63 (0.27), residues: 378 sheet: -0.93 (0.30), residues: 314 loop : -2.02 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 214 HIS 0.005 0.001 HIS B 482 PHE 0.020 0.002 PHE B 577 TYR 0.020 0.002 TYR B 521 ARG 0.010 0.000 ARG B 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 1.308 Fit side-chains REVERT: A 152 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7641 (m-40) REVERT: A 520 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5322 (pm20) REVERT: B 21 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: B 76 MET cc_start: 0.4709 (tpt) cc_final: 0.3883 (ttt) REVERT: B 160 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: B 289 TYR cc_start: 0.8051 (m-80) cc_final: 0.7841 (m-10) REVERT: B 429 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8204 (t80) REVERT: B 488 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8286 (mtpp) REVERT: B 547 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7363 (mpt180) REVERT: B 608 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 637 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7379 (ttp80) outliers start: 47 outliers final: 37 residues processed: 141 average time/residue: 0.2907 time to fit residues: 56.4945 Evaluate side-chains 144 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 152 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 438 SER 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 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 333 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 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 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 31 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109251 restraints weight = 17424.858| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.11 r_work: 0.3138 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11757 Z= 0.187 Angle : 0.581 9.300 16008 Z= 0.307 Chirality : 0.043 0.189 1743 Planarity : 0.004 0.059 1922 Dihedral : 17.029 165.389 1787 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.57 % Allowed : 30.93 % 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 (0.24), residues: 1294 helix: 1.77 (0.27), residues: 377 sheet: -0.74 (0.31), residues: 300 loop : -1.85 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 214 HIS 0.003 0.000 HIS A 482 PHE 0.016 0.001 PHE A 481 TYR 0.018 0.001 TYR B 521 ARG 0.009 0.000 ARG B 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2429.01 seconds wall clock time: 45 minutes 45.89 seconds (2745.89 seconds total)