Starting phenix.real_space_refine on Mon Jul 28 13:09:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dh9_27433/07_2025/8dh9_27433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dh9_27433/07_2025/8dh9_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_27433/07_2025/8dh9_27433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dh9_27433/07_2025/8dh9_27433.map" model { file = "/net/cci-nas-00/data/ceres_data/8dh9_27433/07_2025/8dh9_27433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dh9_27433/07_2025/8dh9_27433.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.71, per 1000 atoms: 0.75 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: 3.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.33 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: 4.28 Time building geometry restraints manager: 3.65 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: 0.010 Normalize map: mean=0, sd=1: 15.140 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.240 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (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 TRP 0.025 0.002 TRP A 756 HIS 0.004 0.001 HIS B 465 PHE 0.014 0.001 PHE B 334 TYR 0.016 0.001 TYR A 424 ARG 0.003 0.000 ARG A 639 Details of bonding type rmsd hydrogen bonds : bond 0.24999 ( 428) hydrogen bonds : angle 8.85174 ( 1224) SS BOND : bond 0.00178 ( 13) SS BOND : angle 0.85942 ( 26) covalent geometry : bond 0.00259 (10482) covalent geometry : angle 0.64947 (14277) *********************** 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 : 0.975 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 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: 0.4828 (m-10) REVERT: A 509 MET cc_start: 0.6869 (tpt) cc_final: 0.6275 (tpt) REVERT: A 510 TRP cc_start: 0.7177 (p90) cc_final: 0.5651 (p90) REVERT: A 580 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7975 (mp10) REVERT: A 693 VAL cc_start: 0.7702 (t) cc_final: 0.7354 (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: 0.7009 (p-90) REVERT: B 428 VAL cc_start: 0.5939 (m) cc_final: 0.5708 (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: 0.7400 (mtpp) REVERT: B 507 TYR cc_start: 0.6530 (m-10) cc_final: 0.6220 (m-10) REVERT: B 530 ASP cc_start: 0.8091 (m-30) cc_final: 0.7878 (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: 0.5515 (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: 0.6154 (p) REVERT: B 795 ILE cc_start: 0.8543 (mt) cc_final: 0.7914 (mt) REVERT: B 814 MET cc_start: 0.4356 (mpp) cc_final: 0.3860 (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: 0.7865 (m-30) REVERT: C 11 LYS cc_start: 0.8654 (mtmm) cc_final: 0.7755 (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: 0.7178 (tp-100) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.2482 time to fit residues: 124.7525 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 : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 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 569 GLN A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 478 HIS B 681 HIS B 685 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.172694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.136607 restraints weight = 32707.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.141163 restraints weight = 20049.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.144133 restraints weight = 13988.404| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10495 Z= 0.189 Angle : 0.716 10.371 14303 Z= 0.380 Chirality : 0.047 0.232 1636 Planarity : 0.006 0.068 1792 Dihedral : 5.078 20.003 1382 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.38 % Favored : 96.39 % Rotamer: Outliers : 0.17 % Allowed : 4.56 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1273 helix: 0.77 (0.34), residues: 217 sheet: 0.22 (0.23), residues: 469 loop : -0.14 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 731 HIS 0.011 0.002 HIS B 584 PHE 0.036 0.002 PHE B 568 TYR 0.023 0.002 TYR A 379 ARG 0.007 0.001 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 428) hydrogen bonds : angle 6.78903 ( 1224) SS BOND : bond 0.01055 ( 13) SS BOND : angle 2.21405 ( 26) covalent geometry : bond 0.00405 (10482) covalent geometry : angle 0.71007 (14277) *********************** 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 332 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 1.249 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: 0.7804 (mp) cc_final: 0.7527 (tp) REVERT: A 341 SER cc_start: 0.8203 (p) cc_final: 0.7830 (m) REVERT: A 369 ASN cc_start: 0.8654 (m-40) cc_final: 0.7333 (t0) REVERT: A 370 LEU cc_start: 0.8277 (mt) cc_final: 0.7853 (mt) REVERT: A 372 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6130 (tm-30) REVERT: A 393 ASN cc_start: 0.7302 (t0) cc_final: 0.6907 (p0) REVERT: A 419 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7632 (mmt-90) REVERT: A 447 TRP cc_start: 0.7630 (p-90) cc_final: 0.7225 (p-90) REVERT: A 448 SER cc_start: 0.8511 (p) cc_final: 0.8248 (t) REVERT: A 468 SER cc_start: 0.2247 (m) cc_final: 0.1332 (t) REVERT: A 478 HIS cc_start: 0.6699 (t-90) cc_final: 0.6467 (t-90) REVERT: A 480 THR cc_start: 0.6694 (m) cc_final: 0.6399 (m) REVERT: A 494 TYR cc_start: 0.5501 (m-80) cc_final: 0.4444 (m-80) REVERT: A 498 PHE cc_start: 0.7194 (t80) cc_final: 0.6640 (t80) REVERT: A 509 MET cc_start: 0.7036 (tpt) cc_final: 0.6751 (tpt) REVERT: A 510 TRP cc_start: 0.7068 (p90) cc_final: 0.5534 (p90) REVERT: A 512 ARG cc_start: 0.5850 (tpp80) cc_final: 0.5315 (tpp80) REVERT: A 539 SER cc_start: 0.7603 (p) cc_final: 0.7355 (t) REVERT: A 553 LYS cc_start: 0.6422 (tppt) cc_final: 0.6201 (tppt) REVERT: A 563 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6326 (mm-30) REVERT: A 578 GLU cc_start: 0.8309 (pm20) cc_final: 0.7497 (pm20) REVERT: A 580 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8025 (mp10) REVERT: A 612 ARG cc_start: 0.7079 (ptp-170) cc_final: 0.6658 (ttp80) REVERT: A 617 LEU cc_start: 0.5569 (mt) cc_final: 0.4855 (pp) REVERT: A 619 TYR cc_start: 0.6942 (m-10) cc_final: 0.6414 (m-10) REVERT: A 643 PHE cc_start: 0.5924 (p90) cc_final: 0.5529 (p90) REVERT: A 681 HIS cc_start: 0.7410 (m-70) cc_final: 0.7178 (m-70) REVERT: A 772 TRP cc_start: 0.7239 (p90) cc_final: 0.7005 (p90) REVERT: A 809 LEU cc_start: 0.8143 (tp) cc_final: 0.7041 (pp) REVERT: A 821 LYS cc_start: 0.7029 (tptm) cc_final: 0.6182 (tttt) REVERT: B 429 ASN cc_start: 0.7518 (t0) cc_final: 0.6969 (t0) REVERT: B 507 TYR cc_start: 0.6459 (m-10) cc_final: 0.6085 (m-10) REVERT: B 544 GLU cc_start: 0.5979 (tp30) cc_final: 0.5553 (tp30) REVERT: B 563 GLU cc_start: 0.6164 (pp20) cc_final: 0.5814 (pp20) REVERT: B 572 TYR cc_start: 0.7038 (p90) cc_final: 0.6651 (p90) REVERT: B 647 MET cc_start: 0.6375 (mmm) cc_final: 0.4863 (tmm) REVERT: B 782 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6435 (pttm) REVERT: B 784 LEU cc_start: 0.7740 (mp) cc_final: 0.7160 (pt) REVERT: B 814 MET cc_start: 0.4714 (mpp) cc_final: 0.4287 (mpp) REVERT: C 54 MET cc_start: 0.8263 (mtm) cc_final: 0.7785 (mmp) REVERT: C 72 ASN cc_start: 0.8031 (p0) cc_final: 0.7354 (p0) REVERT: C 80 LEU cc_start: 0.8339 (tt) cc_final: 0.8015 (tt) REVERT: C 81 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6953 (mm-30) REVERT: C 84 ARG cc_start: 0.8369 (mtp180) cc_final: 0.7059 (ttm170) REVERT: C 85 ASP cc_start: 0.8155 (m-30) cc_final: 0.7592 (m-30) REVERT: C 87 LEU cc_start: 0.8549 (pp) cc_final: 0.8346 (pp) REVERT: C 88 HIS cc_start: 0.7774 (m170) cc_final: 0.7361 (m90) REVERT: C 111 ASP cc_start: 0.7347 (t0) cc_final: 0.6909 (m-30) REVERT: C 120 SER cc_start: 0.8650 (m) cc_final: 0.8281 (p) REVERT: D 160 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7038 (tp40) outliers start: 2 outliers final: 0 residues processed: 331 average time/residue: 0.2720 time to fit residues: 123.1393 Evaluate side-chains 289 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS B 806 GLN ** C 75 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 = 0.4503 r_free = 0.4503 target = 0.171859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.138048 restraints weight = 31967.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.142402 restraints weight = 19455.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.145044 restraints weight = 13488.819| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.4417 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= 0.159 Angle : 0.686 10.383 14303 Z= 0.354 Chirality : 0.047 0.216 1636 Planarity : 0.008 0.257 1792 Dihedral : 5.076 27.181 1382 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.83 % Favored : 96.94 % Rotamer: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1273 helix: 0.70 (0.34), residues: 216 sheet: 0.33 (0.24), residues: 460 loop : -0.19 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 703 HIS 0.004 0.001 HIS B 349 PHE 0.015 0.001 PHE C 41 TYR 0.017 0.002 TYR B 494 ARG 0.032 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 428) hydrogen bonds : angle 6.41219 ( 1224) SS BOND : bond 0.01087 ( 13) SS BOND : angle 1.98568 ( 26) covalent geometry : bond 0.00339 (10482) covalent geometry : angle 0.68125 (14277) *********************** 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 318 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 1.693 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: 0.7864 (mp) cc_final: 0.7479 (tp) REVERT: A 341 SER cc_start: 0.8193 (p) cc_final: 0.7850 (m) REVERT: A 370 LEU cc_start: 0.8125 (mt) cc_final: 0.7780 (mt) REVERT: A 393 ASN cc_start: 0.7142 (t0) cc_final: 0.6769 (p0) REVERT: A 419 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7706 (mmt-90) REVERT: A 426 ILE cc_start: 0.7730 (mm) cc_final: 0.7334 (tp) REVERT: A 444 THR cc_start: 0.7517 (m) cc_final: 0.7208 (p) REVERT: A 478 HIS cc_start: 0.7113 (t-90) cc_final: 0.6793 (t-90) REVERT: A 480 THR cc_start: 0.6867 (m) cc_final: 0.6261 (m) REVERT: A 498 PHE cc_start: 0.6854 (t80) cc_final: 0.6049 (t80) REVERT: A 510 TRP cc_start: 0.6987 (p90) cc_final: 0.5713 (p90) REVERT: A 512 ARG cc_start: 0.6063 (tpp80) cc_final: 0.5338 (tpp80) REVERT: A 539 SER cc_start: 0.7782 (p) cc_final: 0.7538 (t) REVERT: A 578 GLU cc_start: 0.8284 (pm20) cc_final: 0.7621 (pm20) REVERT: A 605 TYR cc_start: 0.7802 (m-80) cc_final: 0.7220 (m-80) REVERT: A 613 ARG cc_start: 0.7996 (tpt90) cc_final: 0.7255 (tpt170) REVERT: A 617 LEU cc_start: 0.5980 (mt) cc_final: 0.5123 (pp) REVERT: A 619 TYR cc_start: 0.6894 (m-10) cc_final: 0.6635 (m-10) REVERT: A 681 HIS cc_start: 0.7408 (m-70) cc_final: 0.7167 (m-70) REVERT: A 767 TYR cc_start: 0.6285 (p90) cc_final: 0.5940 (p90) REVERT: B 437 ASP cc_start: 0.7788 (t0) cc_final: 0.7568 (t0) REVERT: B 439 TYR cc_start: 0.7812 (m-10) cc_final: 0.7578 (m-10) REVERT: B 507 TYR cc_start: 0.6610 (m-10) cc_final: 0.6018 (m-10) REVERT: B 563 GLU cc_start: 0.6103 (pp20) cc_final: 0.5715 (pp20) REVERT: B 567 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7262 (tm-30) REVERT: B 572 TYR cc_start: 0.6991 (p90) cc_final: 0.6629 (p90) REVERT: B 591 SER cc_start: 0.8449 (t) cc_final: 0.8229 (t) REVERT: B 613 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7160 (mtt-85) REVERT: B 614 LEU cc_start: 0.8825 (tt) cc_final: 0.8419 (pt) REVERT: B 647 MET cc_start: 0.6484 (mmm) cc_final: 0.4749 (tmm) REVERT: B 703 TRP cc_start: 0.5652 (t60) cc_final: 0.5013 (t60) REVERT: B 771 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6962 (tp30) REVERT: B 782 LYS cc_start: 0.7599 (mtmm) cc_final: 0.7112 (mtmm) REVERT: B 783 TRP cc_start: 0.5613 (p-90) cc_final: 0.5357 (p-90) REVERT: B 784 LEU cc_start: 0.7919 (mp) cc_final: 0.7323 (pt) REVERT: B 814 MET cc_start: 0.4437 (mpp) cc_final: 0.4027 (mpp) REVERT: C 8 ASP cc_start: 0.8329 (p0) cc_final: 0.7249 (p0) REVERT: C 11 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8059 (mtmm) REVERT: C 54 MET cc_start: 0.8183 (mtm) cc_final: 0.7738 (mmp) REVERT: C 81 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6795 (mm-30) REVERT: C 84 ARG cc_start: 0.8352 (mtp180) cc_final: 0.6904 (ttm170) REVERT: C 85 ASP cc_start: 0.8056 (m-30) cc_final: 0.7512 (m-30) REVERT: C 87 LEU cc_start: 0.8498 (pp) cc_final: 0.8238 (pp) REVERT: C 88 HIS cc_start: 0.7671 (m170) cc_final: 0.7278 (m90) REVERT: C 111 ASP cc_start: 0.7282 (t0) cc_final: 0.6939 (m-30) REVERT: C 120 SER cc_start: 0.8617 (m) cc_final: 0.8128 (p) REVERT: D 160 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7105 (tp40) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.2930 time to fit residues: 129.2466 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 : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 796 HIS B 349 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.169161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.135828 restraints weight = 31409.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.140098 restraints weight = 19229.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.142886 restraints weight = 13314.460| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.5364 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= 0.166 Angle : 0.665 10.039 14303 Z= 0.351 Chirality : 0.046 0.178 1636 Planarity : 0.005 0.053 1792 Dihedral : 5.181 24.978 1382 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1273 helix: 0.52 (0.34), residues: 216 sheet: 0.18 (0.24), residues: 476 loop : -0.31 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 366 HIS 0.005 0.001 HIS B 349 PHE 0.027 0.002 PHE B 568 TYR 0.020 0.002 TYR A 379 ARG 0.018 0.001 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 428) hydrogen bonds : angle 6.24553 ( 1224) SS BOND : bond 0.00807 ( 13) SS BOND : angle 1.74090 ( 26) covalent geometry : bond 0.00347 (10482) covalent geometry : angle 0.66187 (14277) *********************** 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 306 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 1.346 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: 0.7861 (mp) cc_final: 0.7527 (tp) REVERT: A 370 LEU cc_start: 0.8218 (mt) cc_final: 0.7806 (mt) REVERT: A 393 ASN cc_start: 0.7148 (t0) cc_final: 0.6671 (p0) REVERT: A 419 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7841 (mmt90) REVERT: A 443 MET cc_start: 0.5569 (tmm) cc_final: 0.5205 (tmm) REVERT: A 464 TYR cc_start: 0.6277 (p90) cc_final: 0.5678 (p90) REVERT: A 478 HIS cc_start: 0.7211 (t-90) cc_final: 0.6996 (t70) REVERT: A 498 PHE cc_start: 0.6963 (t80) cc_final: 0.6301 (t80) REVERT: A 509 MET cc_start: 0.7373 (tpt) cc_final: 0.6908 (tpt) REVERT: A 510 TRP cc_start: 0.7182 (p90) cc_final: 0.6022 (p90) REVERT: A 533 VAL cc_start: 0.8253 (t) cc_final: 0.8029 (p) REVERT: A 587 PHE cc_start: 0.8173 (m-80) cc_final: 0.7891 (m-80) REVERT: A 605 TYR cc_start: 0.7972 (m-80) cc_final: 0.7594 (m-80) REVERT: A 622 ASN cc_start: 0.7987 (t0) cc_final: 0.7767 (t0) REVERT: A 785 ARG cc_start: 0.7216 (tmm160) cc_final: 0.6852 (tmt170) REVERT: A 821 LYS cc_start: 0.7215 (tttt) cc_final: 0.6980 (tttt) REVERT: B 437 ASP cc_start: 0.8180 (t0) cc_final: 0.7980 (t0) REVERT: B 439 TYR cc_start: 0.7919 (m-10) cc_final: 0.7616 (m-10) REVERT: B 504 LEU cc_start: 0.8609 (tp) cc_final: 0.8260 (mm) REVERT: B 507 TYR cc_start: 0.6559 (m-10) cc_final: 0.5940 (m-10) REVERT: B 545 ILE cc_start: 0.6563 (mp) cc_final: 0.6358 (mp) REVERT: B 572 TYR cc_start: 0.7129 (p90) cc_final: 0.6782 (p90) REVERT: B 591 SER cc_start: 0.8598 (t) cc_final: 0.8287 (p) REVERT: B 613 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7212 (mtt-85) REVERT: B 632 MET cc_start: 0.7426 (tpt) cc_final: 0.6767 (tpt) REVERT: B 647 MET cc_start: 0.6524 (mmm) cc_final: 0.4731 (tmm) REVERT: B 703 TRP cc_start: 0.5611 (t60) cc_final: 0.4974 (t60) REVERT: B 771 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7118 (tp30) REVERT: B 777 GLU cc_start: 0.8010 (mp0) cc_final: 0.7742 (mp0) REVERT: B 782 LYS cc_start: 0.7473 (mtmm) cc_final: 0.7018 (mtmm) REVERT: B 795 ILE cc_start: 0.8541 (mp) cc_final: 0.8254 (mp) REVERT: B 814 MET cc_start: 0.4537 (mpp) cc_final: 0.4111 (mpp) REVERT: C 8 ASP cc_start: 0.8250 (p0) cc_final: 0.7251 (p0) REVERT: C 11 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8036 (mtmm) REVERT: C 54 MET cc_start: 0.8099 (mtm) cc_final: 0.7798 (mmp) REVERT: C 62 GLN cc_start: 0.8157 (tt0) cc_final: 0.7710 (tt0) REVERT: C 81 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6846 (mm-30) REVERT: C 82 ASN cc_start: 0.8025 (m110) cc_final: 0.7727 (m110) REVERT: C 84 ARG cc_start: 0.8467 (mtp180) cc_final: 0.7112 (ttm170) REVERT: C 85 ASP cc_start: 0.8105 (m-30) cc_final: 0.7645 (m-30) REVERT: C 88 HIS cc_start: 0.7886 (m170) cc_final: 0.7121 (m90) REVERT: C 111 ASP cc_start: 0.7498 (t0) cc_final: 0.7212 (m-30) REVERT: C 120 SER cc_start: 0.8670 (m) cc_final: 0.8233 (p) REVERT: C 135 ASP cc_start: 0.7998 (t70) cc_final: 0.7724 (t70) REVERT: D 160 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7115 (tp40) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.2500 time to fit residues: 106.3576 Evaluate side-chains 276 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS A 567 GLN A 796 HIS B 418 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.168881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.135186 restraints weight = 31420.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.139439 restraints weight = 19077.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.142256 restraints weight = 13229.591| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.5974 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= 0.155 Angle : 0.643 10.649 14303 Z= 0.338 Chirality : 0.046 0.171 1636 Planarity : 0.005 0.096 1792 Dihedral : 5.240 29.795 1382 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1273 helix: 0.49 (0.34), residues: 222 sheet: 0.01 (0.23), residues: 494 loop : -0.37 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 447 HIS 0.006 0.001 HIS B 349 PHE 0.023 0.002 PHE B 793 TYR 0.037 0.002 TYR C 61 ARG 0.006 0.001 ARG A 613 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 428) hydrogen bonds : angle 6.06761 ( 1224) SS BOND : bond 0.00312 ( 13) SS BOND : angle 1.22601 ( 26) covalent geometry : bond 0.00337 (10482) covalent geometry : angle 0.64180 (14277) *********************** 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 298 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.222 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: A 338 ILE cc_start: 0.7908 (mp) cc_final: 0.7619 (tp) REVERT: A 365 VAL cc_start: 0.7351 (t) cc_final: 0.7049 (m) REVERT: A 370 LEU cc_start: 0.8266 (mt) cc_final: 0.7998 (mt) REVERT: A 373 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8241 (tmtt) REVERT: A 393 ASN cc_start: 0.7217 (t0) cc_final: 0.6715 (p0) REVERT: A 419 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7931 (mmp-170) REVERT: A 426 ILE cc_start: 0.7858 (mm) cc_final: 0.7479 (tp) REVERT: A 443 MET cc_start: 0.5673 (tmm) cc_final: 0.5431 (tmm) REVERT: A 464 TYR cc_start: 0.6421 (p90) cc_final: 0.5586 (p90) REVERT: A 493 PHE cc_start: 0.7737 (m-80) cc_final: 0.7157 (m-80) REVERT: A 494 TYR cc_start: 0.5831 (m-80) cc_final: 0.5046 (m-80) REVERT: A 498 PHE cc_start: 0.6960 (t80) cc_final: 0.6431 (t80) REVERT: A 501 ILE cc_start: 0.8083 (pt) cc_final: 0.7701 (mp) REVERT: A 509 MET cc_start: 0.7415 (tpt) cc_final: 0.7183 (tpt) REVERT: A 510 TRP cc_start: 0.7362 (p90) cc_final: 0.6680 (p90) REVERT: A 533 VAL cc_start: 0.8357 (t) cc_final: 0.8119 (p) REVERT: A 569 GLN cc_start: 0.6910 (tp40) cc_final: 0.6597 (tp40) REVERT: A 605 TYR cc_start: 0.8010 (m-80) cc_final: 0.7692 (m-80) REVERT: A 619 TYR cc_start: 0.7079 (m-80) cc_final: 0.6747 (m-80) REVERT: A 725 PHE cc_start: 0.6540 (m-80) cc_final: 0.6197 (m-80) REVERT: A 785 ARG cc_start: 0.7323 (tmm160) cc_final: 0.6864 (tmt170) REVERT: B 502 PHE cc_start: 0.5611 (m-80) cc_final: 0.5212 (m-10) REVERT: B 548 ASN cc_start: 0.7755 (m-40) cc_final: 0.7443 (t0) REVERT: B 572 TYR cc_start: 0.7168 (p90) cc_final: 0.6784 (p90) REVERT: B 613 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7313 (mtt-85) REVERT: B 647 MET cc_start: 0.6572 (mmm) cc_final: 0.4806 (tmm) REVERT: B 701 PHE cc_start: 0.6580 (p90) cc_final: 0.6271 (p90) REVERT: B 703 TRP cc_start: 0.5702 (t60) cc_final: 0.4967 (t60) REVERT: B 771 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6935 (tp30) REVERT: B 782 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7190 (mtmm) REVERT: B 814 MET cc_start: 0.4570 (mpp) cc_final: 0.4185 (mpp) REVERT: C 8 ASP cc_start: 0.8314 (p0) cc_final: 0.7259 (p0) REVERT: C 11 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8015 (mtmm) REVERT: C 54 MET cc_start: 0.8096 (mtm) cc_final: 0.7728 (mtt) REVERT: C 62 GLN cc_start: 0.8147 (tt0) cc_final: 0.7380 (tt0) REVERT: C 65 LEU cc_start: 0.8354 (mt) cc_final: 0.8121 (mt) REVERT: C 81 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6421 (mm-30) REVERT: C 82 ASN cc_start: 0.8095 (m110) cc_final: 0.7849 (m110) REVERT: C 84 ARG cc_start: 0.8429 (mtp180) cc_final: 0.6981 (ttm-80) REVERT: C 85 ASP cc_start: 0.8092 (m-30) cc_final: 0.7708 (m-30) REVERT: C 88 HIS cc_start: 0.8002 (m170) cc_final: 0.7096 (m90) REVERT: C 117 SER cc_start: 0.6316 (m) cc_final: 0.4866 (m) REVERT: C 120 SER cc_start: 0.8736 (m) cc_final: 0.8280 (p) REVERT: C 132 SER cc_start: 0.7916 (p) cc_final: 0.7675 (p) REVERT: C 133 LEU cc_start: 0.8480 (mt) cc_final: 0.8236 (mt) REVERT: D 160 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7052 (tp40) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2887 time to fit residues: 119.1324 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 : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 0.1980 chunk 122 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.168660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.133790 restraints weight = 32261.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.138289 restraints weight = 19502.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.141208 restraints weight = 13437.684| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.6367 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= 0.143 Angle : 0.649 10.463 14303 Z= 0.337 Chirality : 0.046 0.225 1636 Planarity : 0.005 0.051 1792 Dihedral : 5.168 31.676 1382 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1273 helix: 0.33 (0.34), residues: 223 sheet: -0.01 (0.23), residues: 492 loop : -0.36 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 447 HIS 0.011 0.001 HIS B 584 PHE 0.021 0.002 PHE B 568 TYR 0.029 0.002 TYR C 61 ARG 0.003 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 428) hydrogen bonds : angle 6.01869 ( 1224) SS BOND : bond 0.00287 ( 13) SS BOND : angle 1.40593 ( 26) covalent geometry : bond 0.00309 (10482) covalent geometry : angle 0.64727 (14277) *********************** 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 296 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 2.560 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: A 338 ILE cc_start: 0.7900 (mp) cc_final: 0.7567 (tp) REVERT: A 372 GLU cc_start: 0.6707 (tm-30) cc_final: 0.6314 (tm-30) REVERT: A 393 ASN cc_start: 0.7173 (t0) cc_final: 0.6017 (p0) REVERT: A 419 ARG cc_start: 0.8282 (mtt180) cc_final: 0.7947 (mmp-170) REVERT: A 443 MET cc_start: 0.5467 (tmm) cc_final: 0.5134 (tmm) REVERT: A 446 ARG cc_start: 0.7476 (tpp80) cc_final: 0.7232 (tpp80) REVERT: A 464 TYR cc_start: 0.6539 (p90) cc_final: 0.5646 (p90) REVERT: A 493 PHE cc_start: 0.7680 (m-80) cc_final: 0.7073 (m-80) REVERT: A 494 TYR cc_start: 0.5588 (m-80) cc_final: 0.5028 (m-80) REVERT: A 497 VAL cc_start: 0.7711 (p) cc_final: 0.6669 (p) REVERT: A 498 PHE cc_start: 0.6997 (t80) cc_final: 0.6626 (t80) REVERT: A 508 THR cc_start: 0.7867 (p) cc_final: 0.7589 (p) REVERT: A 510 TRP cc_start: 0.7338 (p90) cc_final: 0.6808 (p90) REVERT: A 533 VAL cc_start: 0.8420 (t) cc_final: 0.8184 (p) REVERT: A 567 GLN cc_start: 0.7916 (pt0) cc_final: 0.7340 (pt0) REVERT: A 569 GLN cc_start: 0.7045 (tp40) cc_final: 0.6656 (tp40) REVERT: A 605 TYR cc_start: 0.7998 (m-80) cc_final: 0.7709 (m-80) REVERT: A 613 ARG cc_start: 0.8099 (tpt170) cc_final: 0.7890 (tpt170) REVERT: A 655 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6317 (pp20) REVERT: A 725 PHE cc_start: 0.6626 (m-80) cc_final: 0.6275 (m-80) REVERT: A 785 ARG cc_start: 0.7511 (tmm160) cc_final: 0.7200 (tmt170) REVERT: B 437 ASP cc_start: 0.8322 (t0) cc_final: 0.8038 (t0) REVERT: B 439 TYR cc_start: 0.7832 (m-10) cc_final: 0.7568 (m-10) REVERT: B 447 TRP cc_start: 0.6584 (p-90) cc_final: 0.6368 (p-90) REVERT: B 499 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 521 ASP cc_start: 0.7081 (p0) cc_final: 0.6322 (m-30) REVERT: B 528 LEU cc_start: 0.8316 (tp) cc_final: 0.8101 (tp) REVERT: B 530 ASP cc_start: 0.8315 (m-30) cc_final: 0.7889 (m-30) REVERT: B 554 VAL cc_start: 0.8005 (t) cc_final: 0.7628 (t) REVERT: B 556 TRP cc_start: 0.6466 (p90) cc_final: 0.6080 (p90) REVERT: B 572 TYR cc_start: 0.7176 (p90) cc_final: 0.6819 (p90) REVERT: B 613 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7327 (mtt-85) REVERT: B 647 MET cc_start: 0.6553 (mmm) cc_final: 0.4793 (tmm) REVERT: B 701 PHE cc_start: 0.6493 (p90) cc_final: 0.6265 (p90) REVERT: B 703 TRP cc_start: 0.5663 (t60) cc_final: 0.4940 (t60) REVERT: B 771 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7043 (tp30) REVERT: B 777 GLU cc_start: 0.7828 (mp0) cc_final: 0.7619 (mp0) REVERT: B 782 LYS cc_start: 0.7478 (mtmm) cc_final: 0.6913 (mtmm) REVERT: B 791 LYS cc_start: 0.5745 (tmtt) cc_final: 0.5523 (tmtt) REVERT: B 814 MET cc_start: 0.4694 (mpp) cc_final: 0.4269 (mpp) REVERT: C 8 ASP cc_start: 0.8300 (p0) cc_final: 0.7244 (p0) REVERT: C 11 LYS cc_start: 0.8519 (mtmm) cc_final: 0.7955 (mtmm) REVERT: C 13 LEU cc_start: 0.7986 (mt) cc_final: 0.7748 (mt) REVERT: C 54 MET cc_start: 0.7842 (mtm) cc_final: 0.7409 (mtt) REVERT: C 62 GLN cc_start: 0.8133 (tt0) cc_final: 0.7332 (tt0) REVERT: C 75 GLN cc_start: 0.8288 (tt0) cc_final: 0.7386 (tp40) REVERT: C 81 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6736 (mm-30) REVERT: C 82 ASN cc_start: 0.8056 (m110) cc_final: 0.7728 (m110) REVERT: C 84 ARG cc_start: 0.8405 (mtp180) cc_final: 0.6997 (ttm170) REVERT: C 85 ASP cc_start: 0.8042 (m-30) cc_final: 0.7663 (m-30) REVERT: C 88 HIS cc_start: 0.7874 (m170) cc_final: 0.7064 (m90) REVERT: C 117 SER cc_start: 0.6221 (m) cc_final: 0.4689 (m) REVERT: C 120 SER cc_start: 0.8721 (m) cc_final: 0.8277 (p) REVERT: D 160 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7053 (tp40) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2839 time to fit residues: 115.6283 Evaluate side-chains 273 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.165038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.129948 restraints weight = 33921.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.134363 restraints weight = 20664.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.137215 restraints weight = 14419.843| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.7191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10495 Z= 0.200 Angle : 0.721 11.396 14303 Z= 0.379 Chirality : 0.048 0.236 1636 Planarity : 0.006 0.063 1792 Dihedral : 5.636 27.020 1382 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.23), residues: 1273 helix: 0.06 (0.34), residues: 222 sheet: -0.18 (0.24), residues: 481 loop : -0.64 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 756 HIS 0.010 0.001 HIS B 584 PHE 0.024 0.002 PHE A 561 TYR 0.016 0.002 TYR B 405 ARG 0.014 0.001 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 428) hydrogen bonds : angle 6.43826 ( 1224) SS BOND : bond 0.01196 ( 13) SS BOND : angle 1.42411 ( 26) covalent geometry : bond 0.00414 (10482) covalent geometry : angle 0.71870 (14277) *********************** 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 299 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.305 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 337 LYS cc_start: 0.7900 (mptt) cc_final: 0.7601 (mmmt) REVERT: A 338 ILE cc_start: 0.8004 (mp) cc_final: 0.7645 (tp) REVERT: A 393 ASN cc_start: 0.6531 (t0) cc_final: 0.5927 (p0) REVERT: A 444 THR cc_start: 0.7230 (p) cc_final: 0.7006 (p) REVERT: A 446 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6413 (tpp80) REVERT: A 464 TYR cc_start: 0.6664 (p90) cc_final: 0.5746 (p90) REVERT: A 486 CYS cc_start: 0.0906 (p) cc_final: 0.0632 (p) REVERT: A 489 GLN cc_start: 0.7756 (mp10) cc_final: 0.7369 (mp-120) REVERT: A 493 PHE cc_start: 0.7817 (m-80) cc_final: 0.7075 (m-80) REVERT: A 498 PHE cc_start: 0.6706 (t80) cc_final: 0.6503 (t80) REVERT: A 510 TRP cc_start: 0.7388 (p90) cc_final: 0.6948 (p90) REVERT: A 533 VAL cc_start: 0.8397 (t) cc_final: 0.8165 (p) REVERT: A 561 PHE cc_start: 0.7275 (t80) cc_final: 0.7019 (t80) REVERT: A 569 GLN cc_start: 0.7104 (tp40) cc_final: 0.6875 (tp40) REVERT: A 577 LYS cc_start: 0.8200 (mppt) cc_final: 0.7808 (mtmm) REVERT: A 578 GLU cc_start: 0.7772 (pm20) cc_final: 0.7553 (pm20) REVERT: A 592 LYS cc_start: 0.8084 (tttm) cc_final: 0.7500 (mmtt) REVERT: A 605 TYR cc_start: 0.8052 (m-80) cc_final: 0.7789 (m-10) REVERT: A 655 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6540 (pp20) REVERT: A 725 PHE cc_start: 0.6767 (m-80) cc_final: 0.6515 (m-80) REVERT: A 767 TYR cc_start: 0.6647 (p90) cc_final: 0.6266 (p90) REVERT: A 772 TRP cc_start: 0.7121 (p90) cc_final: 0.6471 (p90) REVERT: B 439 TYR cc_start: 0.7825 (m-10) cc_final: 0.7568 (m-10) REVERT: B 447 TRP cc_start: 0.6850 (p-90) cc_final: 0.6392 (p-90) REVERT: B 478 HIS cc_start: 0.6723 (t-90) cc_final: 0.6333 (t-90) REVERT: B 493 PHE cc_start: 0.8236 (m-80) cc_final: 0.7904 (m-80) REVERT: B 499 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8328 (tm-30) REVERT: B 521 ASP cc_start: 0.7021 (p0) cc_final: 0.6410 (m-30) REVERT: B 572 TYR cc_start: 0.7128 (p90) cc_final: 0.6831 (p90) REVERT: B 613 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7363 (ttt-90) REVERT: B 647 MET cc_start: 0.6533 (mmm) cc_final: 0.4645 (tmm) REVERT: B 698 ASN cc_start: 0.6518 (p0) cc_final: 0.6222 (t0) REVERT: B 701 PHE cc_start: 0.6506 (p90) cc_final: 0.6128 (p90) REVERT: B 703 TRP cc_start: 0.5713 (t60) cc_final: 0.4629 (t60) REVERT: B 771 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7175 (tp30) REVERT: B 777 GLU cc_start: 0.7754 (mp0) cc_final: 0.7490 (mp0) REVERT: B 782 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7020 (mttp) REVERT: B 791 LYS cc_start: 0.5773 (tmtt) cc_final: 0.5510 (tmtt) REVERT: B 814 MET cc_start: 0.4860 (mpp) cc_final: 0.4496 (mpp) REVERT: C 7 GLN cc_start: 0.7969 (pp30) cc_final: 0.7108 (pp30) REVERT: C 8 ASP cc_start: 0.8220 (p0) cc_final: 0.6895 (p0) REVERT: C 11 LYS cc_start: 0.8495 (mtmm) cc_final: 0.7896 (mtmm) REVERT: C 54 MET cc_start: 0.7704 (mtm) cc_final: 0.7338 (mtt) REVERT: C 58 LEU cc_start: 0.8425 (mt) cc_final: 0.7988 (mt) REVERT: C 62 GLN cc_start: 0.8241 (tt0) cc_final: 0.7909 (tt0) REVERT: C 75 GLN cc_start: 0.8180 (tt0) cc_final: 0.7842 (tp-100) REVERT: C 81 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6992 (mm-30) REVERT: C 82 ASN cc_start: 0.8070 (m110) cc_final: 0.7787 (m110) REVERT: C 84 ARG cc_start: 0.8420 (mtp180) cc_final: 0.7082 (ttm-80) REVERT: C 85 ASP cc_start: 0.8138 (m-30) cc_final: 0.7791 (m-30) REVERT: C 88 HIS cc_start: 0.7738 (m170) cc_final: 0.7238 (m90) REVERT: C 120 SER cc_start: 0.8824 (m) cc_final: 0.8543 (p) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3024 time to fit residues: 126.7640 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 : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 0.0040 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.166833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.133073 restraints weight = 32360.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.137454 restraints weight = 19679.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.140265 restraints weight = 13529.024| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.7428 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= 0.141 Angle : 0.684 13.114 14303 Z= 0.354 Chirality : 0.047 0.185 1636 Planarity : 0.005 0.053 1792 Dihedral : 5.377 35.982 1382 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1273 helix: 0.27 (0.35), residues: 223 sheet: -0.18 (0.24), residues: 470 loop : -0.62 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 644 HIS 0.007 0.001 HIS B 584 PHE 0.015 0.001 PHE B 568 TYR 0.022 0.001 TYR C 61 ARG 0.008 0.001 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 428) hydrogen bonds : angle 6.13934 ( 1224) SS BOND : bond 0.00623 ( 13) SS BOND : angle 1.79325 ( 26) covalent geometry : bond 0.00302 (10482) covalent geometry : angle 0.68066 (14277) *********************** 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 297 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.259 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: 0.7963 (mp) cc_final: 0.7613 (tp) REVERT: A 372 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6472 (tm-30) REVERT: A 446 ARG cc_start: 0.7097 (tpp80) cc_final: 0.6516 (tpp80) REVERT: A 464 TYR cc_start: 0.6832 (p90) cc_final: 0.5913 (p90) REVERT: A 480 THR cc_start: 0.6914 (m) cc_final: 0.6355 (m) REVERT: A 489 GLN cc_start: 0.7677 (mp10) cc_final: 0.7456 (mp10) REVERT: A 493 PHE cc_start: 0.7923 (m-80) cc_final: 0.7187 (m-80) REVERT: A 496 CYS cc_start: 0.5036 (t) cc_final: 0.4758 (m) REVERT: A 508 THR cc_start: 0.7727 (p) cc_final: 0.7345 (p) REVERT: A 510 TRP cc_start: 0.7368 (p90) cc_final: 0.6770 (p90) REVERT: A 511 ILE cc_start: 0.7916 (mm) cc_final: 0.7694 (mm) REVERT: A 563 GLU cc_start: 0.6784 (pm20) cc_final: 0.6541 (pm20) REVERT: A 569 GLN cc_start: 0.6932 (tp40) cc_final: 0.6486 (tp40) REVERT: A 577 LYS cc_start: 0.8099 (mppt) cc_final: 0.7734 (mtmm) REVERT: A 578 GLU cc_start: 0.7635 (pm20) cc_final: 0.7412 (pm20) REVERT: A 592 LYS cc_start: 0.8045 (tttm) cc_final: 0.7500 (mmtt) REVERT: A 605 TYR cc_start: 0.8022 (m-80) cc_final: 0.7821 (m-10) REVERT: A 655 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6465 (pp20) REVERT: A 725 PHE cc_start: 0.6778 (m-80) cc_final: 0.6486 (m-80) REVERT: A 767 TYR cc_start: 0.6506 (p90) cc_final: 0.6121 (p90) REVERT: A 772 TRP cc_start: 0.7048 (p90) cc_final: 0.6527 (p90) REVERT: B 443 MET cc_start: 0.6597 (tpp) cc_final: 0.6369 (tpp) REVERT: B 447 TRP cc_start: 0.6792 (p-90) cc_final: 0.6353 (p-90) REVERT: B 478 HIS cc_start: 0.6652 (t-90) cc_final: 0.6275 (t-90) REVERT: B 493 PHE cc_start: 0.7752 (m-80) cc_final: 0.7538 (m-80) REVERT: B 511 ILE cc_start: 0.7212 (tp) cc_final: 0.6841 (tp) REVERT: B 521 ASP cc_start: 0.7005 (p0) cc_final: 0.6358 (m-30) REVERT: B 530 ASP cc_start: 0.8588 (m-30) cc_final: 0.8368 (m-30) REVERT: B 555 SER cc_start: 0.7615 (m) cc_final: 0.7393 (m) REVERT: B 572 TYR cc_start: 0.7179 (p90) cc_final: 0.6882 (p90) REVERT: B 613 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7392 (ttt-90) REVERT: B 647 MET cc_start: 0.6466 (mmm) cc_final: 0.4591 (tmm) REVERT: B 701 PHE cc_start: 0.6336 (p90) cc_final: 0.5998 (p90) REVERT: B 703 TRP cc_start: 0.5673 (t60) cc_final: 0.4528 (t60) REVERT: B 771 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7182 (tp30) REVERT: B 777 GLU cc_start: 0.7856 (mp0) cc_final: 0.7571 (mp0) REVERT: B 782 LYS cc_start: 0.7571 (mtmm) cc_final: 0.7206 (mptt) REVERT: B 814 MET cc_start: 0.4726 (mpp) cc_final: 0.4408 (mpp) REVERT: C 7 GLN cc_start: 0.7962 (pp30) cc_final: 0.7230 (pp30) REVERT: C 8 ASP cc_start: 0.8182 (p0) cc_final: 0.6868 (p0) REVERT: C 11 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7770 (mtmm) REVERT: C 53 LYS cc_start: 0.7702 (pttp) cc_final: 0.7466 (pttp) REVERT: C 62 GLN cc_start: 0.8118 (tt0) cc_final: 0.7719 (tt0) REVERT: C 65 LEU cc_start: 0.8210 (mt) cc_final: 0.7951 (mt) REVERT: C 75 GLN cc_start: 0.8376 (tt0) cc_final: 0.7890 (tp-100) REVERT: C 81 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7199 (mm-30) REVERT: C 82 ASN cc_start: 0.8084 (m110) cc_final: 0.7783 (m110) REVERT: C 84 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7069 (ttm-80) REVERT: C 85 ASP cc_start: 0.8112 (m-30) cc_final: 0.7741 (m-30) REVERT: C 88 HIS cc_start: 0.7738 (m170) cc_final: 0.7306 (m90) REVERT: C 120 SER cc_start: 0.8794 (m) cc_final: 0.8535 (p) REVERT: C 132 SER cc_start: 0.7563 (p) cc_final: 0.7327 (p) REVERT: C 134 GLN cc_start: 0.8070 (mp10) cc_final: 0.7845 (mp10) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2955 time to fit residues: 119.5661 Evaluate side-chains 274 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.166792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.132388 restraints weight = 32852.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.136807 restraints weight = 20035.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.139491 restraints weight = 13873.263| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.7766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10495 Z= 0.146 Angle : 0.706 17.212 14303 Z= 0.364 Chirality : 0.047 0.212 1636 Planarity : 0.005 0.081 1792 Dihedral : 5.408 30.386 1382 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1273 helix: 0.29 (0.35), residues: 223 sheet: -0.24 (0.24), residues: 475 loop : -0.56 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 556 HIS 0.007 0.001 HIS B 584 PHE 0.016 0.002 PHE B 568 TYR 0.019 0.001 TYR A 572 ARG 0.010 0.001 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 428) hydrogen bonds : angle 6.03583 ( 1224) SS BOND : bond 0.01005 ( 13) SS BOND : angle 2.41146 ( 26) covalent geometry : bond 0.00320 (10482) covalent geometry : angle 0.69917 (14277) *********************** 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 295 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.172 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: 0.7880 (mp) cc_final: 0.7434 (tp) REVERT: A 372 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6197 (tm-30) REVERT: A 400 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7284 (mtp85) REVERT: A 419 ARG cc_start: 0.8406 (mtt180) cc_final: 0.7814 (mmt-90) REVERT: A 426 ILE cc_start: 0.8070 (mm) cc_final: 0.7832 (mp) REVERT: A 443 MET cc_start: 0.5147 (tmm) cc_final: 0.4380 (tmm) REVERT: A 444 THR cc_start: 0.7591 (p) cc_final: 0.7214 (p) REVERT: A 446 ARG cc_start: 0.7120 (tpp80) cc_final: 0.6365 (tpp80) REVERT: A 447 TRP cc_start: 0.7899 (p-90) cc_final: 0.7248 (p-90) REVERT: A 464 TYR cc_start: 0.6753 (p90) cc_final: 0.6122 (p90) REVERT: A 489 GLN cc_start: 0.7616 (mp10) cc_final: 0.7368 (mp10) REVERT: A 493 PHE cc_start: 0.7881 (m-80) cc_final: 0.7067 (m-80) REVERT: A 498 PHE cc_start: 0.7024 (t80) cc_final: 0.6778 (t80) REVERT: A 509 MET cc_start: 0.7282 (tpt) cc_final: 0.6810 (tpt) REVERT: A 510 TRP cc_start: 0.7240 (p90) cc_final: 0.6287 (p90) REVERT: A 511 ILE cc_start: 0.7904 (mm) cc_final: 0.7658 (mm) REVERT: A 563 GLU cc_start: 0.6941 (pm20) cc_final: 0.6720 (pm20) REVERT: A 569 GLN cc_start: 0.6910 (tp40) cc_final: 0.6656 (tp40) REVERT: A 577 LYS cc_start: 0.8060 (mppt) cc_final: 0.7709 (mtmm) REVERT: A 580 GLN cc_start: 0.8445 (mp10) cc_final: 0.8166 (mm-40) REVERT: A 592 LYS cc_start: 0.8067 (tttm) cc_final: 0.7514 (mmtt) REVERT: A 655 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6539 (pp20) REVERT: A 725 PHE cc_start: 0.6842 (m-80) cc_final: 0.6617 (m-80) REVERT: A 767 TYR cc_start: 0.6547 (p90) cc_final: 0.6334 (p90) REVERT: A 768 LEU cc_start: 0.7975 (mt) cc_final: 0.7425 (mt) REVERT: A 772 TRP cc_start: 0.7068 (p90) cc_final: 0.6538 (p90) REVERT: B 447 TRP cc_start: 0.6864 (p-90) cc_final: 0.6562 (p-90) REVERT: B 478 HIS cc_start: 0.6595 (t-90) cc_final: 0.6258 (t-90) REVERT: B 493 PHE cc_start: 0.7837 (m-80) cc_final: 0.7633 (m-80) REVERT: B 499 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 511 ILE cc_start: 0.7187 (tp) cc_final: 0.6962 (tp) REVERT: B 521 ASP cc_start: 0.6947 (p0) cc_final: 0.6335 (m-30) REVERT: B 572 TYR cc_start: 0.7114 (p90) cc_final: 0.6746 (p90) REVERT: B 582 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7430 (mmmt) REVERT: B 613 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7324 (ttt-90) REVERT: B 639 ARG cc_start: 0.6954 (mmp80) cc_final: 0.6649 (mmp80) REVERT: B 647 MET cc_start: 0.6476 (mmm) cc_final: 0.4584 (tmm) REVERT: B 660 LEU cc_start: 0.7852 (tp) cc_final: 0.7405 (mm) REVERT: B 698 ASN cc_start: 0.6723 (p0) cc_final: 0.6355 (t0) REVERT: B 701 PHE cc_start: 0.6374 (p90) cc_final: 0.5682 (p90) REVERT: B 703 TRP cc_start: 0.5725 (t60) cc_final: 0.4527 (t60) REVERT: B 771 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7224 (tp30) REVERT: B 814 MET cc_start: 0.4575 (mpp) cc_final: 0.4274 (mpp) REVERT: C 7 GLN cc_start: 0.7929 (pp30) cc_final: 0.7107 (pp30) REVERT: C 8 ASP cc_start: 0.8157 (p0) cc_final: 0.6591 (p0) REVERT: C 11 LYS cc_start: 0.8363 (mtmm) cc_final: 0.7730 (mtmm) REVERT: C 53 LYS cc_start: 0.7755 (pttp) cc_final: 0.7359 (pttp) REVERT: C 62 GLN cc_start: 0.8124 (tt0) cc_final: 0.7672 (tt0) REVERT: C 75 GLN cc_start: 0.8364 (tt0) cc_final: 0.7930 (tp-100) REVERT: C 81 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 82 ASN cc_start: 0.8122 (m110) cc_final: 0.7805 (m110) REVERT: C 85 ASP cc_start: 0.8131 (m-30) cc_final: 0.7752 (m-30) REVERT: C 88 HIS cc_start: 0.7779 (m170) cc_final: 0.7551 (m90) REVERT: C 120 SER cc_start: 0.8599 (m) cc_final: 0.8324 (p) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2477 time to fit residues: 99.2448 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 : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 C 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.164744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.131074 restraints weight = 32434.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.135339 restraints weight = 19765.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.138133 restraints weight = 13676.797| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10495 Z= 0.176 Angle : 0.742 15.129 14303 Z= 0.385 Chirality : 0.048 0.226 1636 Planarity : 0.006 0.097 1792 Dihedral : 5.544 24.253 1382 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1273 helix: 0.12 (0.34), residues: 223 sheet: -0.33 (0.24), residues: 480 loop : -0.69 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 644 HIS 0.006 0.001 HIS B 584 PHE 0.039 0.002 PHE B 568 TYR 0.020 0.002 TYR A 605 ARG 0.007 0.001 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 428) hydrogen bonds : angle 6.15000 ( 1224) SS BOND : bond 0.00643 ( 13) SS BOND : angle 2.21094 ( 26) covalent geometry : bond 0.00381 (10482) covalent geometry : angle 0.73621 (14277) ********************** 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 304 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.148 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: A 338 ILE cc_start: 0.7998 (mp) cc_final: 0.7556 (tp) REVERT: A 339 LEU cc_start: 0.8186 (mm) cc_final: 0.7883 (mm) REVERT: A 370 LEU cc_start: 0.7929 (mt) cc_final: 0.7311 (tp) REVERT: A 372 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6098 (tm-30) REVERT: A 426 ILE cc_start: 0.8059 (mm) cc_final: 0.7831 (mp) REVERT: A 443 MET cc_start: 0.5215 (tmm) cc_final: 0.4484 (tmm) REVERT: A 464 TYR cc_start: 0.6850 (p90) cc_final: 0.6079 (p90) REVERT: A 484 LYS cc_start: 0.7711 (tptt) cc_final: 0.6949 (tmtt) REVERT: A 489 GLN cc_start: 0.7931 (mp10) cc_final: 0.7629 (mp10) REVERT: A 493 PHE cc_start: 0.7982 (m-80) cc_final: 0.7265 (m-80) REVERT: A 498 PHE cc_start: 0.7610 (t80) cc_final: 0.7198 (t80) REVERT: A 510 TRP cc_start: 0.7290 (p90) cc_final: 0.6867 (p90) REVERT: A 563 GLU cc_start: 0.6843 (pm20) cc_final: 0.6497 (pm20) REVERT: A 569 GLN cc_start: 0.6912 (tp40) cc_final: 0.6674 (tp40) REVERT: A 577 LYS cc_start: 0.7983 (mppt) cc_final: 0.7676 (mtmm) REVERT: A 580 GLN cc_start: 0.8461 (mp10) cc_final: 0.8200 (mm-40) REVERT: A 592 LYS cc_start: 0.8154 (tttm) cc_final: 0.7623 (mmtt) REVERT: A 632 MET cc_start: 0.1340 (mmm) cc_final: 0.0507 (mmm) REVERT: A 644 TRP cc_start: 0.7415 (t-100) cc_final: 0.6355 (t60) REVERT: A 655 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6519 (pp20) REVERT: A 767 TYR cc_start: 0.6627 (p90) cc_final: 0.6307 (p90) REVERT: A 772 TRP cc_start: 0.6928 (p90) cc_final: 0.6406 (p90) REVERT: B 447 TRP cc_start: 0.6811 (p-90) cc_final: 0.6509 (p-90) REVERT: B 478 HIS cc_start: 0.6464 (t-90) cc_final: 0.6162 (t-90) REVERT: B 493 PHE cc_start: 0.7906 (m-80) cc_final: 0.7387 (m-80) REVERT: B 499 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 512 ARG cc_start: 0.7087 (pmt-80) cc_final: 0.6424 (pmt-80) REVERT: B 572 TYR cc_start: 0.7185 (p90) cc_final: 0.6861 (p90) REVERT: B 582 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7457 (mmmt) REVERT: B 613 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7358 (ttt-90) REVERT: B 647 MET cc_start: 0.6459 (mmm) cc_final: 0.4579 (tmm) REVERT: B 660 LEU cc_start: 0.7777 (tp) cc_final: 0.7303 (mm) REVERT: B 698 ASN cc_start: 0.6493 (p0) cc_final: 0.6198 (t0) REVERT: B 701 PHE cc_start: 0.6336 (p90) cc_final: 0.5601 (p90) REVERT: B 703 TRP cc_start: 0.5722 (t60) cc_final: 0.4553 (t60) REVERT: B 771 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7194 (tp30) REVERT: B 777 GLU cc_start: 0.7735 (mp0) cc_final: 0.7512 (mp0) REVERT: B 782 LYS cc_start: 0.7508 (mtmm) cc_final: 0.7053 (mtmm) REVERT: B 814 MET cc_start: 0.4743 (mpp) cc_final: 0.4426 (mpp) REVERT: C 7 GLN cc_start: 0.7888 (pp30) cc_final: 0.6920 (pp30) REVERT: C 8 ASP cc_start: 0.8139 (p0) cc_final: 0.6694 (p0) REVERT: C 11 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7739 (mtmm) REVERT: C 53 LYS cc_start: 0.7820 (pttp) cc_final: 0.7542 (pttp) REVERT: C 58 LEU cc_start: 0.8595 (mt) cc_final: 0.8187 (mt) REVERT: C 62 GLN cc_start: 0.8179 (tt0) cc_final: 0.7251 (tt0) REVERT: C 75 GLN cc_start: 0.8297 (tt0) cc_final: 0.7958 (tp-100) REVERT: C 81 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6930 (mm-30) REVERT: C 82 ASN cc_start: 0.8218 (m110) cc_final: 0.7942 (m110) REVERT: C 84 ARG cc_start: 0.8444 (mtp180) cc_final: 0.7191 (ttm170) REVERT: C 85 ASP cc_start: 0.8221 (m-30) cc_final: 0.7820 (m-30) REVERT: C 88 HIS cc_start: 0.7811 (m170) cc_final: 0.7325 (m90) REVERT: C 120 SER cc_start: 0.8648 (m) cc_final: 0.8429 (p) REVERT: C 134 GLN cc_start: 0.8138 (mp10) cc_final: 0.7851 (mp10) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2360 time to fit residues: 98.8299 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 : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 117 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 16 optimal weight: 0.0050 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.2792 ------------------------------------------------------------------------------- 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 A 489 GLN C 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.167435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.132911 restraints weight = 33127.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137258 restraints weight = 20166.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.140098 restraints weight = 14016.968| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.8293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10495 Z= 0.132 Angle : 0.713 15.452 14303 Z= 0.366 Chirality : 0.047 0.200 1636 Planarity : 0.006 0.096 1792 Dihedral : 5.221 23.669 1382 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 0.08 % Allowed : 0.34 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1273 helix: 0.33 (0.35), residues: 224 sheet: -0.28 (0.24), residues: 483 loop : -0.68 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 772 HIS 0.004 0.001 HIS B 584 PHE 0.054 0.002 PHE B 568 TYR 0.020 0.001 TYR C 61 ARG 0.015 0.001 ARG B 639 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 428) hydrogen bonds : angle 5.88503 ( 1224) SS BOND : bond 0.00644 ( 13) SS BOND : angle 2.68930 ( 26) covalent geometry : bond 0.00296 (10482) covalent geometry : angle 0.70397 (14277) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5060.68 seconds wall clock time: 93 minutes 10.24 seconds (5590.24 seconds total)