Starting phenix.real_space_refine on Wed Mar 4 03:06:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dh9_27433/03_2026/8dh9_27433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dh9_27433/03_2026/8dh9_27433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dh9_27433/03_2026/8dh9_27433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dh9_27433/03_2026/8dh9_27433.map" model { file = "/net/cci-nas-00/data/ceres_data/8dh9_27433/03_2026/8dh9_27433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dh9_27433/03_2026/8dh9_27433.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 6557 2.51 5 N 1728 2.21 5 O 1895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10229 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3994 Classifications: {'peptide': 495} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 464} Chain: "B" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4025 Classifications: {'peptide': 499} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 468} Chain: "C" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1087 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "D" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 2.41, per 1000 atoms: 0.24 Number of scatterers: 10229 At special positions: 0 Unit cell: (141.96, 140.767, 159.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1895 8.00 N 1728 7.00 C 6557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 496 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.04 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS D 167 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 447.6 milliseconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 20.3% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.712A pdb=" N VAL A 533 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 731 through 735 removed outlier: 3.921A pdb=" N LYS A 735 " --> pdb=" O TRP A 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 731 through 735' Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.559A pdb=" N SER B 454 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.672A pdb=" N VAL B 532 " --> pdb=" O PRO B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'C' and resid 2 through 26 Processing helix chain 'C' and resid 27 through 29 No H-bonds generated for 'chain 'C' and resid 27 through 29' Processing helix chain 'C' and resid 50 through 67 Processing helix chain 'C' and resid 70 through 94 Processing helix chain 'C' and resid 107 through 117 removed outlier: 3.843A pdb=" N ASP C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 141 removed outlier: 4.083A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 49 removed outlier: 3.543A pdb=" N THR D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 129 through 138 removed outlier: 4.183A pdb=" N GLY D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 163 Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.548A pdb=" N ALA A 346 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 389 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 387 " --> pdb=" O CYS A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.511A pdb=" N GLU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 433 through 436 Processing sheet with id=AA6, first strand: chain 'A' and resid 482 through 484 removed outlier: 4.247A pdb=" N LEU A 462 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 482 through 484 removed outlier: 4.247A pdb=" N LEU A 462 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 545 removed outlier: 4.020A pdb=" N VAL A 541 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 555 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA A 543 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A 553 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 545 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU A 551 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 582 through 586 removed outlier: 3.826A pdb=" N PHE A 568 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 643 through 648 removed outlier: 3.532A pdb=" N ASP A 648 " --> pdb=" O ASN A 657 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 688 through 694 removed outlier: 5.609A pdb=" N TYR A 677 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 739 through 746 Processing sheet with id=AB4, first strand: chain 'A' and resid 781 through 787 Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.548A pdb=" N VAL B 389 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 387 " --> pdb=" O CYS B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AB8, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AB9, first strand: chain 'B' and resid 432 through 436 removed outlier: 3.576A pdb=" N CYS B 496 " --> pdb=" O CYS B 445 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP B 447 " --> pdb=" O TYR B 494 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 482 through 484 removed outlier: 3.671A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 482 through 484 removed outlier: 3.671A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 507 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET B 509 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 539 through 545 removed outlier: 5.966A pdb=" N ASN B 540 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU B 557 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 596 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 582 through 586 removed outlier: 3.501A pdb=" N VAL B 607 " --> pdb=" O ALA B 627 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AC6, first strand: chain 'B' and resid 688 through 694 removed outlier: 5.733A pdb=" N TYR B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 743 through 748 removed outlier: 6.260A pdb=" N CYS B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 782 through 787 removed outlier: 3.524A pdb=" N TYR B 767 " --> pdb=" O VAL B 812 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3245 1.34 - 1.46: 2478 1.46 - 1.58: 4692 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 10482 Sorted by residual: bond pdb=" C TRP B 662 " pdb=" N LYS B 663 " ideal model delta sigma weight residual 1.327 1.342 -0.015 1.39e-02 5.18e+03 1.19e+00 bond pdb=" CA SER B 450 " pdb=" C SER B 450 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.18e+00 bond pdb=" N ASN B 393 " pdb=" CA ASN B 393 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.16e+00 bond pdb=" CA ILE D 69 " pdb=" CB ILE D 69 " ideal model delta sigma weight residual 1.539 1.527 0.012 1.18e-02 7.18e+03 1.10e+00 bond pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.94e-01 ... (remaining 10477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 14130 2.51 - 5.02: 131 5.02 - 7.54: 13 7.54 - 10.05: 1 10.05 - 12.56: 2 Bond angle restraints: 14277 Sorted by residual: angle pdb=" C SER A 481 " pdb=" N GLU A 482 " pdb=" CA GLU A 482 " ideal model delta sigma weight residual 122.74 113.82 8.92 2.44e+00 1.68e-01 1.34e+01 angle pdb=" CA LEU A 440 " pdb=" CB LEU A 440 " pdb=" CG LEU A 440 " ideal model delta sigma weight residual 116.30 128.86 -12.56 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CA SER B 450 " pdb=" C SER B 450 " pdb=" N THR B 451 " ideal model delta sigma weight residual 116.84 122.89 -6.05 1.71e+00 3.42e-01 1.25e+01 angle pdb=" CB MET A 781 " pdb=" CG MET A 781 " pdb=" SD MET A 781 " ideal model delta sigma weight residual 112.70 102.51 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N SER D 138 " pdb=" CA SER D 138 " pdb=" C SER D 138 " ideal model delta sigma weight residual 107.32 112.20 -4.88 1.65e+00 3.67e-01 8.75e+00 ... (remaining 14272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5919 17.64 - 35.28: 356 35.28 - 52.92: 52 52.92 - 70.56: 13 70.56 - 88.20: 11 Dihedral angle restraints: 6351 sinusoidal: 2566 harmonic: 3785 Sorted by residual: dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 53.71 39.29 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CB CYS D 117 " pdb=" SG CYS D 117 " pdb=" SG CYS D 167 " pdb=" CB CYS D 167 " ideal model delta sinusoidal sigma weight residual 93.00 60.65 32.35 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 410 " pdb=" CB CYS A 410 " ideal model delta sinusoidal sigma weight residual 93.00 62.06 30.94 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 6348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 979 0.029 - 0.058: 413 0.058 - 0.086: 117 0.086 - 0.115: 107 0.115 - 0.144: 20 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CG LEU A 462 " pdb=" CB LEU A 462 " pdb=" CD1 LEU A 462 " pdb=" CD2 LEU A 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 770 " pdb=" N ILE B 770 " pdb=" C ILE B 770 " pdb=" CB ILE B 770 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1633 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO A 375 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 558 " 0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 559 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 559 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 559 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 756 " -0.011 2.00e-02 2.50e+03 9.13e-03 2.08e+00 pdb=" CG TRP A 756 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 756 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 756 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 756 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 756 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 756 " 0.000 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 168 2.64 - 3.20: 9241 3.20 - 3.77: 16241 3.77 - 4.33: 21882 4.33 - 4.90: 34808 Nonbonded interactions: 82340 Sorted by model distance: nonbonded pdb=" OG SER B 721 " pdb=" OD1 ASN B 724 " model vdw 2.073 3.040 nonbonded pdb=" OE1 GLU B 422 " pdb=" OH TYR B 424 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A 721 " pdb=" OD1 ASN A 724 " model vdw 2.211 3.040 nonbonded pdb=" O ASN D 43 " pdb=" ND1 HIS D 47 " model vdw 2.217 3.120 nonbonded pdb=" OG SER D 91 " pdb=" OD1 ASN D 93 " model vdw 2.244 3.040 ... (remaining 82335 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 332 through 826) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 22 through 162) } 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 group one per residue 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: 2.980 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.810 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10495 Z= 0.136 Angle : 0.650 12.562 14303 Z= 0.355 Chirality : 0.042 0.144 1636 Planarity : 0.004 0.047 1792 Dihedral : 12.032 88.201 3854 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.83 % Favored : 96.94 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1273 helix: 1.25 (0.35), residues: 212 sheet: 0.06 (0.23), residues: 457 loop : 0.20 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 639 TYR 0.016 0.001 TYR A 424 PHE 0.014 0.001 PHE B 334 TRP 0.025 0.002 TRP A 756 HIS 0.004 0.001 HIS B 465 Details of bonding type rmsd covalent geometry : bond 0.00259 (10482) covalent geometry : angle 0.64947 (14277) SS BOND : bond 0.00178 ( 13) SS BOND : angle 0.85942 ( 26) hydrogen bonds : bond 0.24999 ( 428) hydrogen bonds : angle 8.85174 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 PHE cc_start: 0.6781 (m-80) cc_final: 0.6130 (m-80) REVERT: A 391 PHE cc_start: 0.6449 (m-80) cc_final: 0.6179 (m-80) REVERT: A 393 ASN cc_start: 0.7221 (t0) cc_final: 0.6902 (p0) REVERT: A 494 TYR cc_start: 0.5411 (m-80) cc_final: 0.4830 (m-10) REVERT: A 509 MET cc_start: 0.6869 (tpt) cc_final: 0.6276 (tpt) REVERT: A 510 TRP cc_start: 0.7177 (p90) cc_final: 0.5653 (p90) REVERT: A 580 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7976 (mp10) REVERT: A 693 VAL cc_start: 0.7702 (t) cc_final: 0.7355 (p) REVERT: A 768 LEU cc_start: 0.7151 (mt) cc_final: 0.6807 (mt) REVERT: A 783 TRP cc_start: 0.7237 (p-90) cc_final: 0.7010 (p-90) REVERT: B 428 VAL cc_start: 0.5939 (m) cc_final: 0.5709 (m) REVERT: B 429 ASN cc_start: 0.6673 (t0) cc_final: 0.6032 (t0) REVERT: B 484 LYS cc_start: 0.7770 (tptt) cc_final: 0.7401 (mtpp) REVERT: B 507 TYR cc_start: 0.6530 (m-10) cc_final: 0.6219 (m-10) REVERT: B 530 ASP cc_start: 0.8091 (m-30) cc_final: 0.7879 (m-30) REVERT: B 554 VAL cc_start: 0.7587 (t) cc_final: 0.7292 (m) REVERT: B 555 SER cc_start: 0.7074 (p) cc_final: 0.6858 (t) REVERT: B 582 LYS cc_start: 0.7572 (mttt) cc_final: 0.7095 (tptp) REVERT: B 612 ARG cc_start: 0.5827 (ptt180) cc_final: 0.5516 (tmm-80) REVERT: B 628 TYR cc_start: 0.7351 (m-80) cc_final: 0.7048 (m-80) REVERT: B 647 MET cc_start: 0.6224 (mmm) cc_final: 0.5381 (tpp) REVERT: B 743 SER cc_start: 0.6406 (m) cc_final: 0.6153 (p) REVERT: B 795 ILE cc_start: 0.8543 (mt) cc_final: 0.7913 (mt) REVERT: B 814 MET cc_start: 0.4356 (mpp) cc_final: 0.3861 (mpp) REVERT: C 8 ASP cc_start: 0.7854 (p0) cc_final: 0.7354 (p0) REVERT: C 9 ASP cc_start: 0.8356 (m-30) cc_final: 0.7864 (m-30) REVERT: C 11 LYS cc_start: 0.8654 (mtmm) cc_final: 0.7754 (mtmm) REVERT: C 54 MET cc_start: 0.8751 (mtm) cc_final: 0.7903 (mmp) REVERT: C 65 LEU cc_start: 0.8262 (mt) cc_final: 0.8011 (mt) REVERT: C 84 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7215 (ttm-80) REVERT: C 85 ASP cc_start: 0.8360 (m-30) cc_final: 0.7931 (m-30) REVERT: C 86 LEU cc_start: 0.8799 (mm) cc_final: 0.8594 (mm) REVERT: C 88 HIS cc_start: 0.7906 (m90) cc_final: 0.7301 (m90) REVERT: D 153 SER cc_start: 0.6061 (m) cc_final: 0.5734 (p) REVERT: D 160 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7176 (tp-100) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.1105 time to fit residues: 56.2216 Evaluate side-chains 288 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.0980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 478 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 151 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.178795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.142400 restraints weight = 33273.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.147162 restraints weight = 20285.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.150238 restraints weight = 14006.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.152326 restraints weight = 10642.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.153647 restraints weight = 8736.676| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10495 Z= 0.145 Angle : 0.657 10.339 14303 Z= 0.345 Chirality : 0.046 0.279 1636 Planarity : 0.005 0.066 1792 Dihedral : 4.634 20.290 1382 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.14 % Favored : 96.62 % Rotamer: Outliers : 0.25 % Allowed : 3.97 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1273 helix: 1.14 (0.35), residues: 216 sheet: 0.28 (0.23), residues: 465 loop : 0.04 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.029 0.002 TYR B 405 PHE 0.036 0.002 PHE B 568 TRP 0.026 0.002 TRP B 703 HIS 0.005 0.001 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00328 (10482) covalent geometry : angle 0.65034 (14277) SS BOND : bond 0.00803 ( 13) SS BOND : angle 2.20839 ( 26) hydrogen bonds : bond 0.05165 ( 428) hydrogen bonds : angle 6.72609 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 311 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7701 (mp) cc_final: 0.7422 (tp) REVERT: A 341 SER cc_start: 0.8114 (p) cc_final: 0.7695 (m) REVERT: A 370 LEU cc_start: 0.8354 (mt) cc_final: 0.7854 (mt) REVERT: A 391 PHE cc_start: 0.6608 (m-80) cc_final: 0.6312 (m-80) REVERT: A 393 ASN cc_start: 0.7238 (t0) cc_final: 0.6844 (p0) REVERT: A 419 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7647 (mmt-90) REVERT: A 510 TRP cc_start: 0.7079 (p90) cc_final: 0.5413 (p90) REVERT: A 512 ARG cc_start: 0.5797 (tpp80) cc_final: 0.5259 (tpp80) REVERT: A 578 GLU cc_start: 0.8315 (pm20) cc_final: 0.7548 (pm20) REVERT: A 580 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7884 (mp10) REVERT: A 619 TYR cc_start: 0.6460 (m-10) cc_final: 0.6065 (m-10) REVERT: A 681 HIS cc_start: 0.7006 (m-70) cc_final: 0.6636 (m-70) REVERT: A 733 MET cc_start: 0.2544 (ttt) cc_final: 0.2296 (ttt) REVERT: B 429 ASN cc_start: 0.6898 (t0) cc_final: 0.6359 (t0) REVERT: B 437 ASP cc_start: 0.7647 (t0) cc_final: 0.7373 (m-30) REVERT: B 507 TYR cc_start: 0.6366 (m-10) cc_final: 0.6075 (m-10) REVERT: B 530 ASP cc_start: 0.8212 (m-30) cc_final: 0.8000 (m-30) REVERT: B 563 GLU cc_start: 0.5840 (pp20) cc_final: 0.5628 (pp20) REVERT: B 572 TYR cc_start: 0.6726 (p90) cc_final: 0.6123 (p90) REVERT: B 582 LYS cc_start: 0.7248 (mttt) cc_final: 0.7012 (tmtt) REVERT: B 628 TYR cc_start: 0.7301 (m-80) cc_final: 0.7049 (m-80) REVERT: B 647 MET cc_start: 0.6348 (mmm) cc_final: 0.5246 (tpp) REVERT: B 776 ASN cc_start: 0.7192 (m110) cc_final: 0.6972 (m110) REVERT: B 795 ILE cc_start: 0.8488 (mt) cc_final: 0.8068 (mp) REVERT: B 797 ASP cc_start: 0.4850 (t0) cc_final: 0.4617 (m-30) REVERT: B 814 MET cc_start: 0.4435 (mpp) cc_final: 0.3994 (mpp) REVERT: C 54 MET cc_start: 0.8082 (mtm) cc_final: 0.7726 (mtt) REVERT: C 72 ASN cc_start: 0.7734 (p0) cc_final: 0.6791 (p0) REVERT: C 80 LEU cc_start: 0.8203 (tt) cc_final: 0.7831 (tt) REVERT: C 81 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6937 (mm-30) REVERT: C 84 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7300 (ttm170) REVERT: C 85 ASP cc_start: 0.7946 (m-30) cc_final: 0.7474 (m-30) REVERT: C 88 HIS cc_start: 0.7463 (m170) cc_final: 0.7031 (m90) REVERT: C 111 ASP cc_start: 0.7109 (t0) cc_final: 0.6721 (m-30) REVERT: C 120 SER cc_start: 0.8474 (m) cc_final: 0.8066 (p) REVERT: D 160 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6996 (tp-100) outliers start: 3 outliers final: 2 residues processed: 313 average time/residue: 0.1016 time to fit residues: 44.1248 Evaluate side-chains 276 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 2 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS A 608 GLN A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS B 685 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.175639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.141513 restraints weight = 31900.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.145852 restraints weight = 21134.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148888 restraints weight = 13845.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.149010 restraints weight = 11636.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.149402 restraints weight = 10660.861| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10495 Z= 0.144 Angle : 0.681 13.612 14303 Z= 0.355 Chirality : 0.047 0.229 1636 Planarity : 0.007 0.226 1792 Dihedral : 4.818 25.799 1382 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.99 % Favored : 96.78 % Rotamer: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1273 helix: 0.91 (0.34), residues: 216 sheet: 0.33 (0.23), residues: 455 loop : -0.19 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 446 TYR 0.018 0.002 TYR A 379 PHE 0.015 0.002 PHE B 793 TRP 0.015 0.002 TRP A 366 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00309 (10482) covalent geometry : angle 0.67328 (14277) SS BOND : bond 0.00548 ( 13) SS BOND : angle 2.48120 ( 26) hydrogen bonds : bond 0.04450 ( 428) hydrogen bonds : angle 6.28497 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7510 (mp) cc_final: 0.7239 (tp) REVERT: A 341 SER cc_start: 0.8226 (p) cc_final: 0.7911 (m) REVERT: A 366 TRP cc_start: 0.6261 (m100) cc_final: 0.6019 (m100) REVERT: A 372 GLU cc_start: 0.6515 (tm-30) cc_final: 0.6191 (tm-30) REVERT: A 393 ASN cc_start: 0.7080 (t0) cc_final: 0.6725 (p0) REVERT: A 419 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7546 (mmt-90) REVERT: A 478 HIS cc_start: 0.6513 (t-90) cc_final: 0.6249 (t-90) REVERT: A 480 THR cc_start: 0.6793 (m) cc_final: 0.6411 (m) REVERT: A 498 PHE cc_start: 0.7123 (t80) cc_final: 0.6567 (t80) REVERT: A 510 TRP cc_start: 0.7188 (p90) cc_final: 0.6411 (p90) REVERT: A 512 ARG cc_start: 0.5891 (tpp80) cc_final: 0.5295 (tpp80) REVERT: A 539 SER cc_start: 0.7612 (p) cc_final: 0.7104 (t) REVERT: A 578 GLU cc_start: 0.8391 (pm20) cc_final: 0.7832 (pm20) REVERT: A 580 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7987 (mp10) REVERT: A 619 TYR cc_start: 0.6780 (m-10) cc_final: 0.6516 (m-10) REVERT: A 643 PHE cc_start: 0.6241 (p90) cc_final: 0.5981 (p90) REVERT: A 768 LEU cc_start: 0.7482 (mt) cc_final: 0.6792 (mt) REVERT: A 785 ARG cc_start: 0.6666 (tmt170) cc_final: 0.6130 (tmt170) REVERT: A 809 LEU cc_start: 0.8030 (tp) cc_final: 0.6973 (pp) REVERT: A 821 LYS cc_start: 0.7140 (tttp) cc_final: 0.6258 (tttt) REVERT: B 429 ASN cc_start: 0.7477 (t0) cc_final: 0.6983 (t0) REVERT: B 437 ASP cc_start: 0.7917 (t0) cc_final: 0.7619 (t0) REVERT: B 439 TYR cc_start: 0.7918 (m-10) cc_final: 0.7478 (m-10) REVERT: B 499 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 507 TYR cc_start: 0.6467 (m-10) cc_final: 0.6075 (m-10) REVERT: B 544 GLU cc_start: 0.5890 (tp30) cc_final: 0.5549 (tp30) REVERT: B 563 GLU cc_start: 0.6090 (pp20) cc_final: 0.5698 (pp20) REVERT: B 566 LEU cc_start: 0.8405 (pt) cc_final: 0.8170 (pt) REVERT: B 568 PHE cc_start: 0.7572 (m-80) cc_final: 0.7289 (m-80) REVERT: B 572 TYR cc_start: 0.6942 (p90) cc_final: 0.6602 (p90) REVERT: B 647 MET cc_start: 0.6377 (mmm) cc_final: 0.4858 (tmm) REVERT: B 771 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7211 (tp30) REVERT: B 782 LYS cc_start: 0.6972 (mtmm) cc_final: 0.6751 (mtmm) REVERT: B 814 MET cc_start: 0.4658 (mpp) cc_final: 0.4241 (mpp) REVERT: C 72 ASN cc_start: 0.7900 (p0) cc_final: 0.7261 (p0) REVERT: C 80 LEU cc_start: 0.8325 (tt) cc_final: 0.7957 (tt) REVERT: C 81 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6956 (mm-30) REVERT: C 84 ARG cc_start: 0.8349 (mtp180) cc_final: 0.7198 (ttm170) REVERT: C 85 ASP cc_start: 0.8119 (m-30) cc_final: 0.7627 (m-30) REVERT: C 88 HIS cc_start: 0.7691 (m170) cc_final: 0.7341 (m90) REVERT: C 111 ASP cc_start: 0.7325 (t0) cc_final: 0.6982 (m-30) REVERT: D 160 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7159 (tp40) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.1010 time to fit residues: 43.4805 Evaluate side-chains 270 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS B 349 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS C 134 GLN D 28 GLN D 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.137919 restraints weight = 31633.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.141508 restraints weight = 20239.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.144526 restraints weight = 12997.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144650 restraints weight = 11716.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.144835 restraints weight = 9995.727| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10495 Z= 0.181 Angle : 0.685 10.166 14303 Z= 0.360 Chirality : 0.046 0.182 1636 Planarity : 0.005 0.049 1792 Dihedral : 5.151 31.706 1382 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1273 helix: 0.56 (0.34), residues: 217 sheet: 0.21 (0.24), residues: 461 loop : -0.27 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 446 TYR 0.018 0.002 TYR A 379 PHE 0.014 0.002 PHE B 793 TRP 0.017 0.002 TRP B 447 HIS 0.006 0.002 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00386 (10482) covalent geometry : angle 0.68147 (14277) SS BOND : bond 0.00725 ( 13) SS BOND : angle 1.71931 ( 26) hydrogen bonds : bond 0.04225 ( 428) hydrogen bonds : angle 6.28299 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7675 (mp) cc_final: 0.7419 (tp) REVERT: A 341 SER cc_start: 0.8242 (p) cc_final: 0.7922 (m) REVERT: A 393 ASN cc_start: 0.7209 (t0) cc_final: 0.6803 (p0) REVERT: A 400 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.6678 (mtm-85) REVERT: A 419 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7800 (mmt-90) REVERT: A 426 ILE cc_start: 0.7746 (mm) cc_final: 0.7311 (tp) REVERT: A 478 HIS cc_start: 0.7028 (t-90) cc_final: 0.6796 (t-90) REVERT: A 498 PHE cc_start: 0.7337 (t80) cc_final: 0.6603 (t80) REVERT: A 510 TRP cc_start: 0.7079 (p90) cc_final: 0.6533 (p90) REVERT: A 512 ARG cc_start: 0.6022 (tpp80) cc_final: 0.5328 (tpp80) REVERT: A 605 TYR cc_start: 0.7911 (m-80) cc_final: 0.7283 (m-80) REVERT: A 617 LEU cc_start: 0.5636 (mt) cc_final: 0.4862 (pp) REVERT: A 619 TYR cc_start: 0.7103 (m-10) cc_final: 0.6858 (m-10) REVERT: A 681 HIS cc_start: 0.7710 (m-70) cc_final: 0.7423 (m-70) REVERT: A 768 LEU cc_start: 0.7830 (mt) cc_final: 0.7319 (mt) REVERT: A 785 ARG cc_start: 0.6454 (tmt170) cc_final: 0.6226 (tmt170) REVERT: B 392 SER cc_start: 0.6255 (m) cc_final: 0.6018 (t) REVERT: B 437 ASP cc_start: 0.8025 (t0) cc_final: 0.7767 (t0) REVERT: B 439 TYR cc_start: 0.8090 (m-10) cc_final: 0.7652 (m-10) REVERT: B 451 THR cc_start: 0.6804 (p) cc_final: 0.6427 (m) REVERT: B 507 TYR cc_start: 0.6508 (m-10) cc_final: 0.6057 (m-10) REVERT: B 521 ASP cc_start: 0.6920 (p0) cc_final: 0.6344 (m-30) REVERT: B 563 GLU cc_start: 0.6242 (pp20) cc_final: 0.5971 (pp20) REVERT: B 572 TYR cc_start: 0.7076 (p90) cc_final: 0.6666 (p90) REVERT: B 647 MET cc_start: 0.6454 (mmm) cc_final: 0.4768 (tmm) REVERT: B 771 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7131 (tp30) REVERT: B 782 LYS cc_start: 0.6894 (mtmm) cc_final: 0.6407 (mtmm) REVERT: B 795 ILE cc_start: 0.8685 (mp) cc_final: 0.8385 (mp) REVERT: B 814 MET cc_start: 0.4573 (mpp) cc_final: 0.4127 (mpp) REVERT: C 8 ASP cc_start: 0.8071 (p0) cc_final: 0.7187 (p0) REVERT: C 11 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8106 (mtmm) REVERT: C 45 LEU cc_start: 0.7999 (mm) cc_final: 0.7493 (mm) REVERT: C 54 MET cc_start: 0.7374 (mpp) cc_final: 0.7078 (mmp) REVERT: C 62 GLN cc_start: 0.8038 (tt0) cc_final: 0.7738 (tt0) REVERT: C 76 ILE cc_start: 0.8768 (mt) cc_final: 0.8458 (mm) REVERT: C 80 LEU cc_start: 0.8406 (tt) cc_final: 0.8112 (tt) REVERT: C 81 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6899 (mm-30) REVERT: C 84 ARG cc_start: 0.8439 (mtp180) cc_final: 0.7162 (ttm-80) REVERT: C 85 ASP cc_start: 0.8293 (m-30) cc_final: 0.7873 (m-30) REVERT: C 88 HIS cc_start: 0.7801 (m170) cc_final: 0.7393 (m90) REVERT: C 111 ASP cc_start: 0.7451 (t0) cc_final: 0.7092 (m-30) REVERT: C 120 SER cc_start: 0.8744 (m) cc_final: 0.8351 (p) REVERT: D 160 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7157 (tp40) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1019 time to fit residues: 43.9866 Evaluate side-chains 278 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS B 418 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.170663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.137114 restraints weight = 32414.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.140786 restraints weight = 20281.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.144588 restraints weight = 13313.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.144422 restraints weight = 11386.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.144558 restraints weight = 9823.921| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10495 Z= 0.162 Angle : 0.670 11.124 14303 Z= 0.349 Chirality : 0.046 0.179 1636 Planarity : 0.005 0.060 1792 Dihedral : 5.137 26.573 1382 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1273 helix: 0.61 (0.34), residues: 218 sheet: 0.09 (0.24), residues: 472 loop : -0.30 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 612 TYR 0.018 0.002 TYR B 794 PHE 0.021 0.001 PHE B 793 TRP 0.020 0.002 TRP A 772 HIS 0.006 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00343 (10482) covalent geometry : angle 0.66816 (14277) SS BOND : bond 0.00425 ( 13) SS BOND : angle 1.33468 ( 26) hydrogen bonds : bond 0.04240 ( 428) hydrogen bonds : angle 6.12652 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7780 (mp) cc_final: 0.7453 (tp) REVERT: A 393 ASN cc_start: 0.7156 (t0) cc_final: 0.6745 (p0) REVERT: A 419 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7838 (mmt-90) REVERT: A 443 MET cc_start: 0.5482 (tmm) cc_final: 0.5239 (tmm) REVERT: A 464 TYR cc_start: 0.6435 (p90) cc_final: 0.5608 (p90) REVERT: A 465 HIS cc_start: 0.6595 (t-90) cc_final: 0.6354 (t-90) REVERT: A 480 THR cc_start: 0.7038 (m) cc_final: 0.6607 (m) REVERT: A 498 PHE cc_start: 0.7357 (t80) cc_final: 0.6551 (t80) REVERT: A 510 TRP cc_start: 0.7231 (p90) cc_final: 0.6733 (p90) REVERT: A 533 VAL cc_start: 0.8356 (t) cc_final: 0.8102 (p) REVERT: A 569 GLN cc_start: 0.6934 (tp40) cc_final: 0.6520 (tp40) REVERT: A 605 TYR cc_start: 0.7958 (m-80) cc_final: 0.7561 (m-80) REVERT: A 681 HIS cc_start: 0.7792 (m-70) cc_final: 0.7507 (m-70) REVERT: A 767 TYR cc_start: 0.6839 (p90) cc_final: 0.6246 (p90) REVERT: B 392 SER cc_start: 0.6089 (m) cc_final: 0.5846 (t) REVERT: B 405 TYR cc_start: 0.5795 (p90) cc_final: 0.5155 (p90) REVERT: B 439 TYR cc_start: 0.8017 (m-10) cc_final: 0.7563 (m-10) REVERT: B 501 ILE cc_start: 0.7555 (pt) cc_final: 0.7325 (pt) REVERT: B 502 PHE cc_start: 0.5687 (m-80) cc_final: 0.5339 (m-10) REVERT: B 504 LEU cc_start: 0.8592 (tp) cc_final: 0.8325 (mm) REVERT: B 521 ASP cc_start: 0.7214 (p0) cc_final: 0.6284 (m-30) REVERT: B 572 TYR cc_start: 0.7067 (p90) cc_final: 0.6764 (p90) REVERT: B 632 MET cc_start: 0.7558 (tpt) cc_final: 0.6853 (tpt) REVERT: B 647 MET cc_start: 0.6562 (mmm) cc_final: 0.4829 (tmm) REVERT: B 771 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7245 (tp30) REVERT: B 777 GLU cc_start: 0.8070 (mp0) cc_final: 0.7817 (mp0) REVERT: B 782 LYS cc_start: 0.7052 (mtmm) cc_final: 0.6631 (mtmm) REVERT: B 791 LYS cc_start: 0.5792 (tmtt) cc_final: 0.5484 (tptp) REVERT: B 814 MET cc_start: 0.4633 (mpp) cc_final: 0.4219 (mpp) REVERT: C 8 ASP cc_start: 0.8036 (p0) cc_final: 0.7172 (p0) REVERT: C 11 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8096 (mtmm) REVERT: C 58 LEU cc_start: 0.8460 (mt) cc_final: 0.8260 (mt) REVERT: C 65 LEU cc_start: 0.8363 (mt) cc_final: 0.8153 (mt) REVERT: C 75 GLN cc_start: 0.7588 (tp-100) cc_final: 0.7068 (tp-100) REVERT: C 80 LEU cc_start: 0.8439 (tt) cc_final: 0.8230 (tt) REVERT: C 81 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6779 (mm-30) REVERT: C 82 ASN cc_start: 0.8108 (m110) cc_final: 0.7718 (m110) REVERT: C 83 LEU cc_start: 0.8421 (pp) cc_final: 0.8160 (pp) REVERT: C 84 ARG cc_start: 0.8483 (mtp180) cc_final: 0.7386 (ttm170) REVERT: C 85 ASP cc_start: 0.8191 (m-30) cc_final: 0.7813 (m-30) REVERT: C 88 HIS cc_start: 0.7853 (m170) cc_final: 0.7261 (m90) REVERT: C 111 ASP cc_start: 0.7538 (t0) cc_final: 0.7202 (m-30) REVERT: C 120 SER cc_start: 0.8756 (m) cc_final: 0.8441 (p) REVERT: C 132 SER cc_start: 0.8111 (p) cc_final: 0.7679 (p) REVERT: C 133 LEU cc_start: 0.8372 (mm) cc_final: 0.8070 (mm) REVERT: D 160 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7065 (tp40) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1021 time to fit residues: 43.8054 Evaluate side-chains 266 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 0.0040 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 123 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN A 608 GLN A 796 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.170842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.136769 restraints weight = 32372.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.140372 restraints weight = 21230.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.143199 restraints weight = 14240.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.143484 restraints weight = 12178.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.143706 restraints weight = 10956.723| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10495 Z= 0.125 Angle : 0.636 10.441 14303 Z= 0.329 Chirality : 0.045 0.175 1636 Planarity : 0.005 0.056 1792 Dihedral : 4.993 37.202 1382 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1273 helix: 0.84 (0.35), residues: 224 sheet: 0.18 (0.24), residues: 461 loop : -0.40 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 400 TYR 0.016 0.001 TYR C 61 PHE 0.019 0.001 PHE B 793 TRP 0.025 0.002 TRP B 447 HIS 0.004 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00279 (10482) covalent geometry : angle 0.63175 (14277) SS BOND : bond 0.00222 ( 13) SS BOND : angle 1.77042 ( 26) hydrogen bonds : bond 0.03938 ( 428) hydrogen bonds : angle 5.87528 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7723 (mp) cc_final: 0.7450 (tp) REVERT: A 372 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6251 (tm-30) REVERT: A 393 ASN cc_start: 0.7090 (t0) cc_final: 0.6345 (p0) REVERT: A 419 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7842 (mtm180) REVERT: A 443 MET cc_start: 0.5294 (tmm) cc_final: 0.5029 (tmm) REVERT: A 480 THR cc_start: 0.7013 (m) cc_final: 0.6624 (m) REVERT: A 498 PHE cc_start: 0.7299 (t80) cc_final: 0.6490 (t80) REVERT: A 508 THR cc_start: 0.7836 (p) cc_final: 0.7410 (p) REVERT: A 510 TRP cc_start: 0.7151 (p90) cc_final: 0.6588 (p90) REVERT: A 533 VAL cc_start: 0.8210 (t) cc_final: 0.7925 (p) REVERT: A 567 GLN cc_start: 0.8017 (pt0) cc_final: 0.7551 (pt0) REVERT: A 569 GLN cc_start: 0.7040 (tp40) cc_final: 0.6580 (tp40) REVERT: A 605 TYR cc_start: 0.7933 (m-80) cc_final: 0.7635 (m-80) REVERT: A 681 HIS cc_start: 0.7615 (m-70) cc_final: 0.7344 (m-70) REVERT: A 725 PHE cc_start: 0.6510 (m-80) cc_final: 0.6075 (m-80) REVERT: A 767 TYR cc_start: 0.6570 (p90) cc_final: 0.6359 (p90) REVERT: B 392 SER cc_start: 0.6218 (m) cc_final: 0.6003 (t) REVERT: B 447 TRP cc_start: 0.6696 (p-90) cc_final: 0.6324 (p-90) REVERT: B 499 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 502 PHE cc_start: 0.5628 (m-80) cc_final: 0.5239 (m-10) REVERT: B 555 SER cc_start: 0.6509 (t) cc_final: 0.6127 (m) REVERT: B 556 TRP cc_start: 0.6526 (p90) cc_final: 0.6253 (p90) REVERT: B 572 TYR cc_start: 0.7028 (p90) cc_final: 0.6716 (p90) REVERT: B 612 ARG cc_start: 0.6596 (ptt180) cc_final: 0.5213 (tmm-80) REVERT: B 632 MET cc_start: 0.7468 (tpt) cc_final: 0.6791 (tpt) REVERT: B 647 MET cc_start: 0.6550 (mmm) cc_final: 0.4876 (tmm) REVERT: B 725 PHE cc_start: 0.7739 (m-10) cc_final: 0.7485 (m-10) REVERT: B 771 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7219 (tp30) REVERT: B 777 GLU cc_start: 0.8036 (mp0) cc_final: 0.7805 (mp0) REVERT: B 782 LYS cc_start: 0.7112 (mtmm) cc_final: 0.6758 (mtmm) REVERT: B 814 MET cc_start: 0.4560 (mpp) cc_final: 0.4179 (mpp) REVERT: C 8 ASP cc_start: 0.8155 (p0) cc_final: 0.7282 (p0) REVERT: C 11 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8089 (mtmm) REVERT: C 54 MET cc_start: 0.8162 (mtm) cc_final: 0.7700 (mmp) REVERT: C 81 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6908 (mm-30) REVERT: C 82 ASN cc_start: 0.8115 (m110) cc_final: 0.7904 (m110) REVERT: C 84 ARG cc_start: 0.8423 (mtp180) cc_final: 0.7227 (ttm-80) REVERT: C 85 ASP cc_start: 0.8055 (m-30) cc_final: 0.7709 (m-30) REVERT: C 88 HIS cc_start: 0.7944 (m170) cc_final: 0.7314 (m90) REVERT: C 120 SER cc_start: 0.8689 (m) cc_final: 0.8302 (p) REVERT: C 132 SER cc_start: 0.7737 (p) cc_final: 0.7401 (p) REVERT: C 133 LEU cc_start: 0.8355 (mm) cc_final: 0.8081 (mm) REVERT: D 160 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7080 (tp40) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1037 time to fit residues: 42.7847 Evaluate side-chains 269 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 72 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.167650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.132513 restraints weight = 32648.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.136982 restraints weight = 20003.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.139888 restraints weight = 13973.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.141782 restraints weight = 10738.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.143004 restraints weight = 8887.617| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10495 Z= 0.169 Angle : 0.677 9.230 14303 Z= 0.356 Chirality : 0.046 0.209 1636 Planarity : 0.005 0.052 1792 Dihedral : 5.119 24.654 1382 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1273 helix: 0.52 (0.34), residues: 223 sheet: 0.12 (0.24), residues: 461 loop : -0.50 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 446 TYR 0.028 0.002 TYR C 61 PHE 0.021 0.002 PHE B 793 TRP 0.019 0.002 TRP B 447 HIS 0.007 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00359 (10482) covalent geometry : angle 0.67552 (14277) SS BOND : bond 0.00463 ( 13) SS BOND : angle 1.32590 ( 26) hydrogen bonds : bond 0.04230 ( 428) hydrogen bonds : angle 6.09820 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.8284 (mt) cc_final: 0.8049 (mt) REVERT: A 373 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8073 (tmtt) REVERT: A 393 ASN cc_start: 0.7328 (t0) cc_final: 0.6496 (p0) REVERT: A 419 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7857 (mmt90) REVERT: A 432 ILE cc_start: 0.8012 (tp) cc_final: 0.7812 (tp) REVERT: A 444 THR cc_start: 0.7535 (p) cc_final: 0.7081 (p) REVERT: A 464 TYR cc_start: 0.6730 (p90) cc_final: 0.5765 (p90) REVERT: A 493 PHE cc_start: 0.7697 (m-80) cc_final: 0.7308 (m-80) REVERT: A 498 PHE cc_start: 0.7163 (t80) cc_final: 0.6358 (t80) REVERT: A 501 ILE cc_start: 0.8229 (pt) cc_final: 0.7789 (mp) REVERT: A 508 THR cc_start: 0.7749 (p) cc_final: 0.7476 (p) REVERT: A 510 TRP cc_start: 0.7257 (p90) cc_final: 0.6816 (p90) REVERT: A 533 VAL cc_start: 0.8283 (t) cc_final: 0.8057 (p) REVERT: A 553 LYS cc_start: 0.6861 (tptt) cc_final: 0.6442 (tptt) REVERT: A 561 PHE cc_start: 0.7317 (t80) cc_final: 0.6892 (t80) REVERT: A 569 GLN cc_start: 0.7023 (tp40) cc_final: 0.6592 (tp40) REVERT: A 577 LYS cc_start: 0.8202 (mppt) cc_final: 0.7807 (mtmm) REVERT: A 605 TYR cc_start: 0.7942 (m-80) cc_final: 0.7717 (m-80) REVERT: A 725 PHE cc_start: 0.6607 (m-80) cc_final: 0.6326 (m-80) REVERT: A 767 TYR cc_start: 0.6434 (p90) cc_final: 0.6207 (p90) REVERT: B 392 SER cc_start: 0.6401 (m) cc_final: 0.6161 (t) REVERT: B 405 TYR cc_start: 0.5754 (p90) cc_final: 0.4930 (p90) REVERT: B 447 TRP cc_start: 0.6508 (p-90) cc_final: 0.6221 (p-90) REVERT: B 499 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 503 LEU cc_start: 0.7732 (mm) cc_final: 0.7496 (mm) REVERT: B 504 LEU cc_start: 0.8545 (tp) cc_final: 0.8266 (mm) REVERT: B 555 SER cc_start: 0.6580 (t) cc_final: 0.6193 (m) REVERT: B 556 TRP cc_start: 0.6437 (p90) cc_final: 0.5721 (p90) REVERT: B 572 TYR cc_start: 0.6993 (p90) cc_final: 0.6703 (p90) REVERT: B 612 ARG cc_start: 0.6678 (ptt180) cc_final: 0.5046 (tmm-80) REVERT: B 647 MET cc_start: 0.6387 (mmm) cc_final: 0.4569 (tmm) REVERT: B 701 PHE cc_start: 0.6471 (p90) cc_final: 0.6091 (p90) REVERT: B 771 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7302 (tp30) REVERT: B 777 GLU cc_start: 0.8158 (mp0) cc_final: 0.7781 (mp0) REVERT: B 782 LYS cc_start: 0.7303 (mtmm) cc_final: 0.6713 (mtmm) REVERT: B 814 MET cc_start: 0.4630 (mpp) cc_final: 0.4210 (mpp) REVERT: C 8 ASP cc_start: 0.8068 (p0) cc_final: 0.7195 (p0) REVERT: C 11 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8062 (mtmm) REVERT: C 55 ASP cc_start: 0.7105 (t70) cc_final: 0.6783 (t0) REVERT: C 65 LEU cc_start: 0.8449 (mt) cc_final: 0.8235 (mt) REVERT: C 81 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6739 (mm-30) REVERT: C 82 ASN cc_start: 0.8113 (m110) cc_final: 0.7822 (m110) REVERT: C 84 ARG cc_start: 0.8586 (mtp180) cc_final: 0.7224 (ttm170) REVERT: C 85 ASP cc_start: 0.8173 (m-30) cc_final: 0.7712 (m-30) REVERT: C 88 HIS cc_start: 0.7834 (m170) cc_final: 0.7062 (m90) REVERT: C 120 SER cc_start: 0.8782 (m) cc_final: 0.8325 (p) REVERT: C 132 SER cc_start: 0.7675 (p) cc_final: 0.7332 (p) REVERT: C 133 LEU cc_start: 0.8325 (mm) cc_final: 0.8003 (mm) REVERT: C 139 GLN cc_start: 0.8219 (tm-30) cc_final: 0.8012 (tm-30) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1027 time to fit residues: 44.3222 Evaluate side-chains 279 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.0000 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 102 optimal weight: 0.0170 chunk 110 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 overall best weight: 0.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.169301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.133866 restraints weight = 32936.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.138427 restraints weight = 20117.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.141459 restraints weight = 13998.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.143324 restraints weight = 10765.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.144640 restraints weight = 8952.523| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10495 Z= 0.127 Angle : 0.656 10.340 14303 Z= 0.337 Chirality : 0.046 0.170 1636 Planarity : 0.005 0.050 1792 Dihedral : 5.027 33.403 1382 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1273 helix: 0.69 (0.35), residues: 223 sheet: 0.16 (0.24), residues: 459 loop : -0.45 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.015 0.001 TYR B 405 PHE 0.020 0.001 PHE B 793 TRP 0.020 0.002 TRP B 447 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00282 (10482) covalent geometry : angle 0.65367 (14277) SS BOND : bond 0.00404 ( 13) SS BOND : angle 1.45726 ( 26) hydrogen bonds : bond 0.03856 ( 428) hydrogen bonds : angle 5.92370 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7883 (mp) cc_final: 0.7489 (tp) REVERT: A 372 GLU cc_start: 0.6481 (tm-30) cc_final: 0.6142 (tm-30) REVERT: A 373 LYS cc_start: 0.8412 (tmtt) cc_final: 0.8173 (tmtt) REVERT: A 393 ASN cc_start: 0.6889 (t0) cc_final: 0.6379 (p0) REVERT: A 419 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7958 (mtm-85) REVERT: A 447 TRP cc_start: 0.8084 (p-90) cc_final: 0.7424 (p-90) REVERT: A 464 TYR cc_start: 0.6635 (p90) cc_final: 0.5750 (p90) REVERT: A 480 THR cc_start: 0.6807 (m) cc_final: 0.6347 (m) REVERT: A 493 PHE cc_start: 0.7716 (m-80) cc_final: 0.7328 (m-80) REVERT: A 498 PHE cc_start: 0.6741 (t80) cc_final: 0.6101 (t80) REVERT: A 508 THR cc_start: 0.7720 (p) cc_final: 0.7245 (p) REVERT: A 510 TRP cc_start: 0.7118 (p90) cc_final: 0.6490 (p90) REVERT: A 511 ILE cc_start: 0.7680 (tp) cc_final: 0.7351 (mm) REVERT: A 553 LYS cc_start: 0.6764 (tptt) cc_final: 0.6417 (tptt) REVERT: A 569 GLN cc_start: 0.6929 (tp40) cc_final: 0.6599 (tp40) REVERT: A 577 LYS cc_start: 0.8198 (mppt) cc_final: 0.7835 (mtmm) REVERT: A 605 TYR cc_start: 0.7994 (m-80) cc_final: 0.7770 (m-80) REVERT: A 613 ARG cc_start: 0.8100 (tpt90) cc_final: 0.7795 (tpt170) REVERT: A 725 PHE cc_start: 0.6686 (m-80) cc_final: 0.6397 (m-80) REVERT: A 767 TYR cc_start: 0.6419 (p90) cc_final: 0.6193 (p90) REVERT: A 789 ASN cc_start: 0.8027 (p0) cc_final: 0.7809 (p0) REVERT: A 821 LYS cc_start: 0.7459 (tttt) cc_final: 0.7114 (ttmt) REVERT: B 392 SER cc_start: 0.6501 (m) cc_final: 0.6241 (t) REVERT: B 405 TYR cc_start: 0.5676 (p90) cc_final: 0.5454 (p90) REVERT: B 447 TRP cc_start: 0.6536 (p-90) cc_final: 0.6316 (p-90) REVERT: B 499 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 502 PHE cc_start: 0.5773 (m-80) cc_final: 0.5364 (m-10) REVERT: B 504 LEU cc_start: 0.8508 (tp) cc_final: 0.8268 (mm) REVERT: B 555 SER cc_start: 0.6608 (t) cc_final: 0.6055 (m) REVERT: B 556 TRP cc_start: 0.6387 (p90) cc_final: 0.5694 (p90) REVERT: B 572 TYR cc_start: 0.7041 (p90) cc_final: 0.6799 (p90) REVERT: B 647 MET cc_start: 0.6412 (mmm) cc_final: 0.4600 (tmm) REVERT: B 701 PHE cc_start: 0.6430 (p90) cc_final: 0.6027 (p90) REVERT: B 771 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7365 (tp30) REVERT: B 777 GLU cc_start: 0.8078 (mp0) cc_final: 0.7783 (mp0) REVERT: B 782 LYS cc_start: 0.7166 (mtmm) cc_final: 0.6664 (mtmm) REVERT: B 814 MET cc_start: 0.4551 (mpp) cc_final: 0.4217 (mpp) REVERT: B 819 LYS cc_start: 0.7168 (tmtt) cc_final: 0.6025 (mtmt) REVERT: C 8 ASP cc_start: 0.8027 (p0) cc_final: 0.7141 (p0) REVERT: C 11 LYS cc_start: 0.8524 (mtmm) cc_final: 0.7994 (mtmm) REVERT: C 55 ASP cc_start: 0.7198 (t70) cc_final: 0.6899 (t70) REVERT: C 65 LEU cc_start: 0.8235 (mt) cc_final: 0.8008 (mt) REVERT: C 75 GLN cc_start: 0.7786 (mm110) cc_final: 0.7575 (mm-40) REVERT: C 81 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7120 (mm-30) REVERT: C 82 ASN cc_start: 0.8224 (m110) cc_final: 0.7980 (m110) REVERT: C 83 LEU cc_start: 0.8365 (pp) cc_final: 0.8133 (pp) REVERT: C 84 ARG cc_start: 0.8488 (mtp180) cc_final: 0.7334 (ttm170) REVERT: C 85 ASP cc_start: 0.8076 (m-30) cc_final: 0.7629 (m-30) REVERT: C 88 HIS cc_start: 0.7764 (m170) cc_final: 0.7154 (m90) REVERT: C 120 SER cc_start: 0.8694 (m) cc_final: 0.8419 (p) REVERT: C 132 SER cc_start: 0.7789 (p) cc_final: 0.7481 (p) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1066 time to fit residues: 44.2060 Evaluate side-chains 281 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS B 608 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.167624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.132979 restraints weight = 32741.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.137474 restraints weight = 19813.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.140334 restraints weight = 13773.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.142197 restraints weight = 10586.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.143487 restraints weight = 8794.776| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.7196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10495 Z= 0.144 Angle : 0.692 11.484 14303 Z= 0.354 Chirality : 0.046 0.181 1636 Planarity : 0.005 0.095 1792 Dihedral : 5.091 31.482 1382 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1273 helix: 0.54 (0.35), residues: 223 sheet: -0.03 (0.25), residues: 436 loop : -0.55 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 105 TYR 0.016 0.001 TYR C 61 PHE 0.019 0.001 PHE A 561 TRP 0.021 0.002 TRP A 756 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00311 (10482) covalent geometry : angle 0.68999 (14277) SS BOND : bond 0.00245 ( 13) SS BOND : angle 1.37165 ( 26) hydrogen bonds : bond 0.04094 ( 428) hydrogen bonds : angle 5.95476 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7944 (mp) cc_final: 0.7594 (tp) REVERT: A 372 GLU cc_start: 0.6674 (tm-30) cc_final: 0.6241 (tm-30) REVERT: A 393 ASN cc_start: 0.6923 (t0) cc_final: 0.6377 (p0) REVERT: A 464 TYR cc_start: 0.6654 (p90) cc_final: 0.5668 (p90) REVERT: A 480 THR cc_start: 0.6907 (m) cc_final: 0.6463 (m) REVERT: A 493 PHE cc_start: 0.7692 (m-80) cc_final: 0.7286 (m-80) REVERT: A 508 THR cc_start: 0.7572 (p) cc_final: 0.7164 (p) REVERT: A 510 TRP cc_start: 0.7233 (p90) cc_final: 0.6761 (p90) REVERT: A 511 ILE cc_start: 0.7720 (tp) cc_final: 0.7378 (mm) REVERT: A 553 LYS cc_start: 0.6755 (tptt) cc_final: 0.6430 (tptt) REVERT: A 569 GLN cc_start: 0.6871 (tp40) cc_final: 0.6442 (tp40) REVERT: A 577 LYS cc_start: 0.8105 (mppt) cc_final: 0.7722 (mtmm) REVERT: A 580 GLN cc_start: 0.8398 (mp10) cc_final: 0.8112 (mm-40) REVERT: A 605 TYR cc_start: 0.8082 (m-80) cc_final: 0.7769 (m-10) REVERT: A 613 ARG cc_start: 0.8155 (tpt90) cc_final: 0.7855 (tpt170) REVERT: A 725 PHE cc_start: 0.6764 (m-80) cc_final: 0.6516 (m-80) REVERT: A 767 TYR cc_start: 0.6460 (p90) cc_final: 0.6205 (p90) REVERT: A 821 LYS cc_start: 0.7425 (tttt) cc_final: 0.7022 (ttmt) REVERT: B 392 SER cc_start: 0.6446 (m) cc_final: 0.6192 (t) REVERT: B 405 TYR cc_start: 0.5702 (p90) cc_final: 0.5488 (p90) REVERT: B 447 TRP cc_start: 0.6500 (p-90) cc_final: 0.6180 (p-90) REVERT: B 499 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 555 SER cc_start: 0.6685 (t) cc_final: 0.6238 (m) REVERT: B 556 TRP cc_start: 0.6446 (p90) cc_final: 0.5583 (p90) REVERT: B 647 MET cc_start: 0.6393 (mmm) cc_final: 0.4444 (tmm) REVERT: B 701 PHE cc_start: 0.6385 (p90) cc_final: 0.5968 (p90) REVERT: B 733 MET cc_start: 0.5413 (ptm) cc_final: 0.4526 (tmm) REVERT: B 771 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7432 (tp30) REVERT: B 777 GLU cc_start: 0.8110 (mp0) cc_final: 0.7820 (mp0) REVERT: B 782 LYS cc_start: 0.7194 (mtmm) cc_final: 0.6679 (mtmm) REVERT: B 814 MET cc_start: 0.4535 (mpp) cc_final: 0.4203 (mpp) REVERT: C 7 GLN cc_start: 0.7885 (pp30) cc_final: 0.6966 (pp30) REVERT: C 8 ASP cc_start: 0.8019 (p0) cc_final: 0.7071 (p0) REVERT: C 11 LYS cc_start: 0.8467 (mtmm) cc_final: 0.7919 (mtmm) REVERT: C 13 LEU cc_start: 0.7846 (mt) cc_final: 0.7645 (mt) REVERT: C 54 MET cc_start: 0.8146 (mtm) cc_final: 0.7777 (mmt) REVERT: C 55 ASP cc_start: 0.7152 (t70) cc_final: 0.6816 (t70) REVERT: C 58 LEU cc_start: 0.8465 (mt) cc_final: 0.8123 (mt) REVERT: C 65 LEU cc_start: 0.8323 (mt) cc_final: 0.8089 (mt) REVERT: C 68 LEU cc_start: 0.8870 (mt) cc_final: 0.8658 (tt) REVERT: C 75 GLN cc_start: 0.8005 (mm110) cc_final: 0.7713 (mm-40) REVERT: C 81 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7200 (mm-30) REVERT: C 82 ASN cc_start: 0.8263 (m110) cc_final: 0.8055 (m110) REVERT: C 83 LEU cc_start: 0.8402 (pp) cc_final: 0.8180 (pp) REVERT: C 84 ARG cc_start: 0.8563 (mtp180) cc_final: 0.7429 (ttm-80) REVERT: C 85 ASP cc_start: 0.8147 (m-30) cc_final: 0.7698 (m-30) REVERT: C 88 HIS cc_start: 0.7820 (m170) cc_final: 0.7274 (m90) REVERT: C 120 SER cc_start: 0.8741 (m) cc_final: 0.8458 (p) REVERT: C 132 SER cc_start: 0.7769 (p) cc_final: 0.7505 (m) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1009 time to fit residues: 41.1078 Evaluate side-chains 277 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS B 608 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.165946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.131261 restraints weight = 32340.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.135641 restraints weight = 19856.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.138509 restraints weight = 13955.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.140374 restraints weight = 10759.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.141478 restraints weight = 8912.034| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10495 Z= 0.149 Angle : 0.697 11.982 14303 Z= 0.361 Chirality : 0.046 0.199 1636 Planarity : 0.005 0.093 1792 Dihedral : 5.228 24.488 1382 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1273 helix: 0.46 (0.34), residues: 223 sheet: -0.04 (0.25), residues: 440 loop : -0.62 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 105 TYR 0.015 0.001 TYR A 379 PHE 0.014 0.001 PHE A 498 TRP 0.025 0.002 TRP A 447 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00325 (10482) covalent geometry : angle 0.69432 (14277) SS BOND : bond 0.00356 ( 13) SS BOND : angle 1.51386 ( 26) hydrogen bonds : bond 0.04154 ( 428) hydrogen bonds : angle 6.01539 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.8031 (mp) cc_final: 0.7695 (tp) REVERT: A 372 GLU cc_start: 0.6544 (tm-30) cc_final: 0.6167 (tm-30) REVERT: A 373 LYS cc_start: 0.8398 (tmmt) cc_final: 0.8191 (tmtt) REVERT: A 374 ILE cc_start: 0.7529 (mt) cc_final: 0.7147 (mt) REVERT: A 393 ASN cc_start: 0.7050 (t0) cc_final: 0.6437 (p0) REVERT: A 443 MET cc_start: 0.5314 (ttm) cc_final: 0.4356 (ttt) REVERT: A 464 TYR cc_start: 0.6707 (p90) cc_final: 0.5798 (p90) REVERT: A 484 LYS cc_start: 0.7799 (tptt) cc_final: 0.7313 (tppt) REVERT: A 493 PHE cc_start: 0.7731 (m-80) cc_final: 0.7466 (m-80) REVERT: A 510 TRP cc_start: 0.7205 (p90) cc_final: 0.6834 (p90) REVERT: A 511 ILE cc_start: 0.7780 (tp) cc_final: 0.7476 (mm) REVERT: A 553 LYS cc_start: 0.6700 (tptt) cc_final: 0.6389 (tptt) REVERT: A 569 GLN cc_start: 0.6916 (tp40) cc_final: 0.6574 (tp40) REVERT: A 577 LYS cc_start: 0.8021 (mppt) cc_final: 0.7666 (mtmm) REVERT: A 580 GLN cc_start: 0.8411 (mp10) cc_final: 0.8200 (mm-40) REVERT: A 605 TYR cc_start: 0.8172 (m-80) cc_final: 0.7889 (m-10) REVERT: A 725 PHE cc_start: 0.6903 (m-80) cc_final: 0.6659 (m-80) REVERT: A 767 TYR cc_start: 0.6577 (p90) cc_final: 0.6287 (p90) REVERT: A 821 LYS cc_start: 0.7393 (tttt) cc_final: 0.7156 (ttmt) REVERT: B 392 SER cc_start: 0.6587 (m) cc_final: 0.6325 (t) REVERT: B 443 MET cc_start: 0.6536 (tpp) cc_final: 0.6261 (tpp) REVERT: B 447 TRP cc_start: 0.6713 (p-90) cc_final: 0.6324 (p-90) REVERT: B 499 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 555 SER cc_start: 0.6671 (t) cc_final: 0.6267 (m) REVERT: B 556 TRP cc_start: 0.6265 (p90) cc_final: 0.5489 (p90) REVERT: B 572 TYR cc_start: 0.6950 (p90) cc_final: 0.6739 (p90) REVERT: B 639 ARG cc_start: 0.6832 (mmp80) cc_final: 0.6538 (mmp80) REVERT: B 647 MET cc_start: 0.6379 (mmm) cc_final: 0.4508 (tmm) REVERT: B 660 LEU cc_start: 0.7795 (tp) cc_final: 0.7556 (mm) REVERT: B 733 MET cc_start: 0.5249 (ptm) cc_final: 0.4636 (tmm) REVERT: B 771 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7436 (tp30) REVERT: B 777 GLU cc_start: 0.8178 (mp0) cc_final: 0.7893 (mp0) REVERT: B 782 LYS cc_start: 0.7127 (mtmm) cc_final: 0.6652 (mtmm) REVERT: B 791 LYS cc_start: 0.5839 (tptp) cc_final: 0.5586 (mmmt) REVERT: B 814 MET cc_start: 0.4543 (mpp) cc_final: 0.4217 (mpp) REVERT: B 819 LYS cc_start: 0.7205 (tmtt) cc_final: 0.6401 (mttt) REVERT: C 8 ASP cc_start: 0.7979 (p0) cc_final: 0.7022 (p0) REVERT: C 11 LYS cc_start: 0.8496 (mtmm) cc_final: 0.7922 (mtmm) REVERT: C 55 ASP cc_start: 0.7187 (t70) cc_final: 0.6983 (t70) REVERT: C 58 LEU cc_start: 0.8342 (mt) cc_final: 0.7987 (mt) REVERT: C 65 LEU cc_start: 0.8378 (mt) cc_final: 0.8140 (mt) REVERT: C 68 LEU cc_start: 0.8930 (mt) cc_final: 0.8657 (tt) REVERT: C 75 GLN cc_start: 0.8268 (mm110) cc_final: 0.7996 (mm-40) REVERT: C 81 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7021 (mm-30) REVERT: C 82 ASN cc_start: 0.8230 (m110) cc_final: 0.7951 (m110) REVERT: C 84 ARG cc_start: 0.8594 (mtp180) cc_final: 0.7479 (ttm170) REVERT: C 85 ASP cc_start: 0.8255 (m-30) cc_final: 0.7794 (m-30) REVERT: C 88 HIS cc_start: 0.7865 (m170) cc_final: 0.7300 (m90) REVERT: C 120 SER cc_start: 0.8786 (m) cc_final: 0.8531 (p) REVERT: D 105 ARG cc_start: 0.6562 (mtp-110) cc_final: 0.6022 (mmt180) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1050 time to fit residues: 43.3583 Evaluate side-chains 281 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN C 75 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.165903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.130756 restraints weight = 33624.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.135220 restraints weight = 20630.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.138106 restraints weight = 14478.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.139923 restraints weight = 11203.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.141278 restraints weight = 9362.151| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.7986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 10495 Z= 0.162 Angle : 0.743 17.203 14303 Z= 0.382 Chirality : 0.048 0.278 1636 Planarity : 0.005 0.089 1792 Dihedral : 5.330 24.510 1382 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1273 helix: 0.42 (0.34), residues: 223 sheet: -0.15 (0.25), residues: 440 loop : -0.63 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 105 TYR 0.020 0.002 TYR B 572 PHE 0.024 0.002 PHE B 498 TRP 0.024 0.002 TRP A 447 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00360 (10482) covalent geometry : angle 0.73805 (14277) SS BOND : bond 0.00580 ( 13) SS BOND : angle 2.20023 ( 26) hydrogen bonds : bond 0.04336 ( 428) hydrogen bonds : angle 6.03245 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.04 seconds wall clock time: 40 minutes 36.13 seconds (2436.13 seconds total)