Starting phenix.real_space_refine on Fri Feb 14 15:53:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dh9_27433/02_2025/8dh9_27433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dh9_27433/02_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_27433/02_2025/8dh9_27433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dh9_27433/02_2025/8dh9_27433.map" model { file = "/net/cci-nas-00/data/ceres_data/8dh9_27433/02_2025/8dh9_27433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dh9_27433/02_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-5592/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: 6.18, per 1000 atoms: 0.60 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 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: 1.39 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: 3.81 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3245 1.34 - 1.46: 2478 1.46 - 1.58: 4692 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 10482 Sorted by residual: bond pdb=" C TRP B 662 " pdb=" N LYS B 663 " ideal model delta sigma weight residual 1.327 1.342 -0.015 1.39e-02 5.18e+03 1.19e+00 bond pdb=" CA SER B 450 " pdb=" C SER B 450 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.18e+00 bond pdb=" N ASN B 393 " pdb=" CA ASN B 393 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.16e+00 bond pdb=" CA ILE D 69 " pdb=" CB ILE D 69 " ideal model delta sigma weight residual 1.539 1.527 0.012 1.18e-02 7.18e+03 1.10e+00 bond pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.94e-01 ... (remaining 10477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 14130 2.51 - 5.02: 131 5.02 - 7.54: 13 7.54 - 10.05: 1 10.05 - 12.56: 2 Bond angle restraints: 14277 Sorted by residual: angle pdb=" C SER A 481 " pdb=" N GLU A 482 " pdb=" CA GLU A 482 " ideal model delta sigma weight residual 122.74 113.82 8.92 2.44e+00 1.68e-01 1.34e+01 angle pdb=" CA LEU A 440 " pdb=" CB LEU A 440 " pdb=" CG LEU A 440 " ideal model delta sigma weight residual 116.30 128.86 -12.56 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CA SER B 450 " pdb=" C SER B 450 " pdb=" N THR B 451 " ideal model delta sigma weight residual 116.84 122.89 -6.05 1.71e+00 3.42e-01 1.25e+01 angle pdb=" CB MET A 781 " pdb=" CG MET A 781 " pdb=" SD MET A 781 " ideal model delta sigma weight residual 112.70 102.51 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N SER D 138 " pdb=" CA SER D 138 " pdb=" C SER D 138 " ideal model delta sigma weight residual 107.32 112.20 -4.88 1.65e+00 3.67e-01 8.75e+00 ... (remaining 14272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5919 17.64 - 35.28: 356 35.28 - 52.92: 52 52.92 - 70.56: 13 70.56 - 88.20: 11 Dihedral angle restraints: 6351 sinusoidal: 2566 harmonic: 3785 Sorted by residual: dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 53.71 39.29 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CB CYS D 117 " pdb=" SG CYS D 117 " pdb=" SG CYS D 167 " pdb=" CB CYS D 167 " ideal model delta sinusoidal sigma weight residual 93.00 60.65 32.35 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 410 " pdb=" CB CYS A 410 " ideal model delta sinusoidal sigma weight residual 93.00 62.06 30.94 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 6348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 979 0.029 - 0.058: 413 0.058 - 0.086: 117 0.086 - 0.115: 107 0.115 - 0.144: 20 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CG LEU A 462 " pdb=" CB LEU A 462 " pdb=" CD1 LEU A 462 " pdb=" CD2 LEU A 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 770 " pdb=" N ILE B 770 " pdb=" C ILE B 770 " pdb=" CB ILE B 770 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1633 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO A 375 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 558 " 0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 559 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 559 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 559 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 756 " -0.011 2.00e-02 2.50e+03 9.13e-03 2.08e+00 pdb=" CG TRP A 756 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 756 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 756 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 756 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 756 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 756 " 0.000 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 168 2.64 - 3.20: 9241 3.20 - 3.77: 16241 3.77 - 4.33: 21882 4.33 - 4.90: 34808 Nonbonded interactions: 82340 Sorted by model distance: nonbonded pdb=" OG SER B 721 " pdb=" OD1 ASN B 724 " model vdw 2.073 3.040 nonbonded pdb=" OE1 GLU B 422 " pdb=" OH TYR B 424 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A 721 " pdb=" OD1 ASN A 724 " model vdw 2.211 3.040 nonbonded pdb=" O ASN D 43 " pdb=" ND1 HIS D 47 " model vdw 2.217 3.120 nonbonded pdb=" OG SER D 91 " pdb=" OD1 ASN D 93 " model vdw 2.244 3.040 ... (remaining 82335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 332 through 826) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 22 through 162) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.200 ------------------------------------------------------------------------------- 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 10482 Z= 0.170 Angle : 0.649 12.562 14277 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 *********************** 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 : 1.168 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: 0.2581 time to fit residues: 130.6241 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 : 1.141 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS B 685 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 151 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.169246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.133775 restraints weight = 32559.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.138089 restraints weight = 20045.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.141000 restraints weight = 14053.866| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10482 Z= 0.332 Angle : 0.782 10.164 14277 Z= 0.420 Chirality : 0.048 0.196 1636 Planarity : 0.007 0.069 1792 Dihedral : 5.467 20.183 1382 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.61 % Favored : 96.15 % Rotamer: Outliers : 0.51 % Allowed : 4.99 % Favored : 94.51 % 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: -0.11 (0.23), residues: 1273 helix: 0.55 (0.33), residues: 215 sheet: 0.02 (0.23), residues: 467 loop : -0.24 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 703 HIS 0.012 0.002 HIS B 584 PHE 0.034 0.002 PHE B 568 TYR 0.025 0.002 TYR A 379 ARG 0.007 0.001 ARG A 645 *********************** 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 340 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 334 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7916 (mp) cc_final: 0.7604 (tp) REVERT: A 341 SER cc_start: 0.8273 (p) cc_final: 0.7909 (m) REVERT: A 369 ASN cc_start: 0.8714 (m-40) cc_final: 0.7766 (t0) REVERT: A 372 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5950 (tm-30) REVERT: A 393 ASN cc_start: 0.7220 (t0) cc_final: 0.6890 (p0) REVERT: A 394 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7181 (pp) REVERT: A 447 TRP cc_start: 0.7711 (p-90) cc_final: 0.6934 (p-90) REVERT: A 448 SER cc_start: 0.8623 (p) cc_final: 0.8366 (t) REVERT: A 494 TYR cc_start: 0.5644 (m-80) cc_final: 0.5376 (m-80) REVERT: A 498 PHE cc_start: 0.7196 (t80) cc_final: 0.6603 (t80) REVERT: A 509 MET cc_start: 0.7079 (tpt) cc_final: 0.6747 (tpt) REVERT: A 510 TRP cc_start: 0.7089 (p90) cc_final: 0.5742 (p90) REVERT: A 512 ARG cc_start: 0.5937 (tpp80) cc_final: 0.5340 (tpp80) REVERT: A 578 GLU cc_start: 0.8256 (pm20) cc_final: 0.7463 (pm20) REVERT: A 580 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8038 (mp10) REVERT: A 605 TYR cc_start: 0.7842 (m-80) cc_final: 0.7296 (m-80) REVERT: A 613 ARG cc_start: 0.8291 (tpt90) cc_final: 0.7686 (tpt170) REVERT: A 617 LEU cc_start: 0.5954 (mt) cc_final: 0.5240 (pp) REVERT: A 619 TYR cc_start: 0.7086 (m-10) cc_final: 0.6805 (m-10) REVERT: A 681 HIS cc_start: 0.7569 (m-70) cc_final: 0.7120 (m-70) REVERT: A 685 HIS cc_start: 0.4626 (OUTLIER) cc_final: 0.3320 (t-170) REVERT: A 733 MET cc_start: 0.3396 (ttt) cc_final: 0.3183 (ttt) REVERT: A 753 ILE cc_start: 0.7885 (mm) cc_final: 0.7672 (tp) REVERT: A 768 LEU cc_start: 0.7855 (mt) cc_final: 0.7506 (mt) REVERT: B 507 TYR cc_start: 0.6544 (m-10) cc_final: 0.6101 (m-10) REVERT: B 521 ASP cc_start: 0.6381 (m-30) cc_final: 0.6061 (p0) REVERT: B 563 GLU cc_start: 0.6317 (pp20) cc_final: 0.5964 (pp20) REVERT: B 572 TYR cc_start: 0.7029 (p90) cc_final: 0.6658 (p90) REVERT: B 591 SER cc_start: 0.8367 (t) cc_final: 0.8105 (t) REVERT: B 647 MET cc_start: 0.6332 (mmm) cc_final: 0.4849 (tmm) REVERT: B 782 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6304 (pttm) REVERT: B 784 LEU cc_start: 0.7837 (mp) cc_final: 0.7150 (pt) REVERT: B 814 MET cc_start: 0.4809 (mpp) cc_final: 0.4374 (mpp) REVERT: C 8 ASP cc_start: 0.8111 (p0) cc_final: 0.7486 (p0) REVERT: C 11 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8093 (mtmm) REVERT: C 45 LEU cc_start: 0.8002 (mm) cc_final: 0.7491 (mm) REVERT: C 54 MET cc_start: 0.8228 (mtm) cc_final: 0.7912 (mmp) REVERT: C 80 LEU cc_start: 0.8393 (tt) cc_final: 0.8145 (tt) REVERT: C 81 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6806 (mm-30) REVERT: C 84 ARG cc_start: 0.8392 (mtp180) cc_final: 0.7065 (ttm170) REVERT: C 85 ASP cc_start: 0.8174 (m-30) cc_final: 0.7677 (m-30) REVERT: C 87 LEU cc_start: 0.8546 (pp) cc_final: 0.8324 (pp) REVERT: C 88 HIS cc_start: 0.7806 (m170) cc_final: 0.7440 (m90) REVERT: C 111 ASP cc_start: 0.7463 (t0) cc_final: 0.7058 (m-30) REVERT: C 120 SER cc_start: 0.8772 (m) cc_final: 0.8466 (m) REVERT: D 160 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6970 (tp40) outliers start: 6 outliers final: 1 residues processed: 338 average time/residue: 0.2412 time to fit residues: 111.9282 Evaluate side-chains 300 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 296 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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: 4.9990 chunk 7 optimal weight: 0.0270 chunk 105 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 98 optimal weight: 0.0170 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS A 478 HIS A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS B 681 HIS B 806 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.173087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.137073 restraints weight = 32059.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.141541 restraints weight = 19709.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144471 restraints weight = 13773.588| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10482 Z= 0.198 Angle : 0.668 10.886 14277 Z= 0.341 Chirality : 0.047 0.304 1636 Planarity : 0.005 0.053 1792 Dihedral : 4.994 24.688 1382 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.04 % 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: 0.12 (0.23), residues: 1273 helix: 0.66 (0.34), residues: 217 sheet: 0.33 (0.23), residues: 472 loop : -0.22 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 366 HIS 0.008 0.001 HIS B 584 PHE 0.012 0.001 PHE C 41 TYR 0.015 0.001 TYR B 494 ARG 0.006 0.001 ARG B 463 *********************** 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 316 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7911 (mp) cc_final: 0.7538 (tp) REVERT: A 341 SER cc_start: 0.8161 (p) cc_final: 0.7831 (m) REVERT: A 370 LEU cc_start: 0.8241 (mt) cc_final: 0.7735 (mt) REVERT: A 393 ASN cc_start: 0.7242 (t0) cc_final: 0.6826 (p0) REVERT: A 419 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7738 (mmt-90) REVERT: A 426 ILE cc_start: 0.7652 (mm) cc_final: 0.7236 (tp) REVERT: A 478 HIS cc_start: 0.6566 (t-90) cc_final: 0.6309 (t-90) REVERT: A 480 THR cc_start: 0.6693 (m) cc_final: 0.6272 (m) REVERT: A 494 TYR cc_start: 0.5545 (m-80) cc_final: 0.5223 (m-80) REVERT: A 498 PHE cc_start: 0.6945 (t80) cc_final: 0.6398 (t80) REVERT: A 508 THR cc_start: 0.8057 (p) cc_final: 0.7667 (p) REVERT: A 510 TRP cc_start: 0.7140 (p90) cc_final: 0.5676 (p90) REVERT: A 512 ARG cc_start: 0.5948 (tpp80) cc_final: 0.5245 (tpp80) REVERT: A 578 GLU cc_start: 0.8241 (pm20) cc_final: 0.7532 (pm20) REVERT: A 605 TYR cc_start: 0.7861 (m-80) cc_final: 0.7371 (m-80) REVERT: A 613 ARG cc_start: 0.8201 (tpt90) cc_final: 0.7523 (tpt170) REVERT: A 617 LEU cc_start: 0.5912 (mt) cc_final: 0.5093 (pp) REVERT: A 619 TYR cc_start: 0.6939 (m-10) cc_final: 0.6656 (m-10) REVERT: A 753 ILE cc_start: 0.7812 (mm) cc_final: 0.7583 (tp) REVERT: A 767 TYR cc_start: 0.6605 (p90) cc_final: 0.6056 (p90) REVERT: B 507 TYR cc_start: 0.6617 (m-10) cc_final: 0.5937 (m-10) REVERT: B 544 GLU cc_start: 0.6057 (tp30) cc_final: 0.5719 (tp30) REVERT: B 545 ILE cc_start: 0.6408 (mp) cc_final: 0.6205 (mp) REVERT: B 563 GLU cc_start: 0.6232 (pp20) cc_final: 0.5842 (pp20) REVERT: B 566 LEU cc_start: 0.8543 (pt) cc_final: 0.8337 (pt) REVERT: B 591 SER cc_start: 0.8479 (t) cc_final: 0.8198 (t) REVERT: B 613 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7300 (mtt-85) REVERT: B 632 MET cc_start: 0.7375 (tpt) cc_final: 0.6738 (tpt) REVERT: B 647 MET cc_start: 0.6450 (mmm) cc_final: 0.4764 (tmm) REVERT: B 771 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6820 (tp30) REVERT: B 782 LYS cc_start: 0.7240 (mtmm) cc_final: 0.6940 (mtmm) REVERT: B 795 ILE cc_start: 0.8620 (mp) cc_final: 0.8170 (mp) REVERT: B 814 MET cc_start: 0.4543 (mpp) cc_final: 0.4148 (mpp) REVERT: C 8 ASP cc_start: 0.8152 (p0) cc_final: 0.7297 (p0) REVERT: C 11 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8041 (mtmm) REVERT: C 54 MET cc_start: 0.8142 (mtm) cc_final: 0.7663 (mmp) REVERT: C 72 ASN cc_start: 0.7692 (p0) cc_final: 0.7108 (p0) REVERT: C 80 LEU cc_start: 0.8354 (tt) cc_final: 0.8144 (tt) REVERT: C 81 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6965 (mm-30) REVERT: C 84 ARG cc_start: 0.8380 (mtp180) cc_final: 0.6873 (ttm-80) REVERT: C 85 ASP cc_start: 0.8054 (m-30) cc_final: 0.7496 (m-30) REVERT: C 87 LEU cc_start: 0.8481 (pp) cc_final: 0.8204 (pp) REVERT: C 88 HIS cc_start: 0.7724 (m170) cc_final: 0.7241 (m90) REVERT: C 111 ASP cc_start: 0.7348 (t0) cc_final: 0.6948 (m-30) REVERT: C 117 SER cc_start: 0.7409 (t) cc_final: 0.6890 (m) REVERT: C 120 SER cc_start: 0.8607 (m) cc_final: 0.8364 (p) REVERT: D 160 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7046 (tp40) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.2547 time to fit residues: 109.4532 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 : 1.165 ------------------------------------------------------------------------------- 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: 3.9990 chunk 111 optimal weight: 0.7980 chunk 20 optimal weight: 0.0030 chunk 24 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS B 349 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 43 ASN D 151 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.169558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.134073 restraints weight = 32170.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.138541 restraints weight = 19802.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.141417 restraints weight = 13804.070| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10482 Z= 0.244 Angle : 0.668 10.127 14277 Z= 0.348 Chirality : 0.046 0.240 1636 Planarity : 0.005 0.051 1792 Dihedral : 5.157 28.192 1382 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.23), residues: 1273 helix: 0.60 (0.34), residues: 216 sheet: 0.09 (0.23), residues: 484 loop : -0.33 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 447 HIS 0.006 0.001 HIS B 584 PHE 0.028 0.002 PHE B 568 TYR 0.037 0.002 TYR C 61 ARG 0.007 0.001 ARG D 105 *********************** 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 302 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.060 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: 0.7976 (mp) cc_final: 0.7643 (tp) REVERT: A 341 SER cc_start: 0.8184 (p) cc_final: 0.7955 (m) REVERT: A 393 ASN cc_start: 0.7214 (t0) cc_final: 0.6753 (p0) REVERT: A 419 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7931 (mtm180) REVERT: A 494 TYR cc_start: 0.5478 (m-80) cc_final: 0.4847 (m-10) REVERT: A 498 PHE cc_start: 0.6932 (t80) cc_final: 0.6454 (t80) REVERT: A 509 MET cc_start: 0.7302 (tpt) cc_final: 0.6842 (tpt) REVERT: A 510 TRP cc_start: 0.7210 (p90) cc_final: 0.5978 (p90) REVERT: A 533 VAL cc_start: 0.8356 (t) cc_final: 0.8117 (p) REVERT: A 587 PHE cc_start: 0.8099 (m-80) cc_final: 0.7850 (m-80) REVERT: A 605 TYR cc_start: 0.7917 (m-80) cc_final: 0.7607 (m-80) REVERT: A 617 LEU cc_start: 0.6292 (mt) cc_final: 0.5516 (pp) REVERT: A 681 HIS cc_start: 0.7617 (m-70) cc_final: 0.7373 (m-70) REVERT: A 753 ILE cc_start: 0.7936 (mm) cc_final: 0.7706 (tp) REVERT: A 767 TYR cc_start: 0.6757 (p90) cc_final: 0.6395 (p90) REVERT: B 437 ASP cc_start: 0.7992 (t0) cc_final: 0.7738 (t0) REVERT: B 439 TYR cc_start: 0.7894 (m-10) cc_final: 0.7638 (m-10) REVERT: B 545 ILE cc_start: 0.6566 (mp) cc_final: 0.6360 (mp) REVERT: B 553 LYS cc_start: 0.8054 (tppt) cc_final: 0.7650 (tptp) REVERT: B 567 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 591 SER cc_start: 0.8596 (t) cc_final: 0.8357 (p) REVERT: B 632 MET cc_start: 0.7514 (tpt) cc_final: 0.6908 (tpt) REVERT: B 647 MET cc_start: 0.6481 (mmm) cc_final: 0.4699 (tmm) REVERT: B 771 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7177 (tp30) REVERT: B 782 LYS cc_start: 0.7086 (mtmm) cc_final: 0.6716 (mtmm) REVERT: B 814 MET cc_start: 0.4606 (mpp) cc_final: 0.4187 (mpp) REVERT: C 8 ASP cc_start: 0.8190 (p0) cc_final: 0.7476 (p0) REVERT: C 11 LYS cc_start: 0.8480 (mtmm) cc_final: 0.8015 (mtmm) REVERT: C 13 LEU cc_start: 0.7884 (mt) cc_final: 0.7678 (mt) REVERT: C 55 ASP cc_start: 0.7275 (t70) cc_final: 0.6958 (t0) REVERT: C 58 LEU cc_start: 0.8216 (mt) cc_final: 0.7837 (mt) REVERT: C 62 GLN cc_start: 0.8202 (tt0) cc_final: 0.7902 (tt0) REVERT: C 81 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6846 (mm-30) REVERT: C 84 ARG cc_start: 0.8499 (mtp180) cc_final: 0.6941 (ttm-80) REVERT: C 85 ASP cc_start: 0.8111 (m-30) cc_final: 0.7634 (m-30) REVERT: C 87 LEU cc_start: 0.8529 (pp) cc_final: 0.8314 (pp) REVERT: C 88 HIS cc_start: 0.7864 (m170) cc_final: 0.7005 (m90) REVERT: C 111 ASP cc_start: 0.7503 (t0) cc_final: 0.7213 (m-30) REVERT: C 120 SER cc_start: 0.8629 (m) cc_final: 0.8383 (m) REVERT: C 132 SER cc_start: 0.7992 (p) cc_final: 0.7777 (p) REVERT: C 133 LEU cc_start: 0.8502 (mt) cc_final: 0.8220 (mt) REVERT: C 134 GLN cc_start: 0.8424 (mp-120) cc_final: 0.7514 (mp10) REVERT: D 160 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7081 (tp40) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2435 time to fit residues: 101.6402 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 : 1.313 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 122 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 567 GLN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN A 796 HIS B 418 HIS B 567 GLN D 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.167169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.133850 restraints weight = 31432.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.138144 restraints weight = 19044.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.140996 restraints weight = 13115.021| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10482 Z= 0.227 Angle : 0.661 11.149 14277 Z= 0.347 Chirality : 0.046 0.181 1636 Planarity : 0.005 0.053 1792 Dihedral : 5.273 23.427 1382 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: -0.30 (0.23), residues: 1273 helix: 0.55 (0.34), residues: 223 sheet: -0.09 (0.23), residues: 501 loop : -0.47 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 644 HIS 0.008 0.001 HIS B 349 PHE 0.021 0.002 PHE B 568 TYR 0.021 0.002 TYR C 61 ARG 0.014 0.001 ARG A 613 *********************** 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 300 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7977 (mp) cc_final: 0.7659 (tp) REVERT: A 370 LEU cc_start: 0.8179 (mt) cc_final: 0.7901 (mt) REVERT: A 393 ASN cc_start: 0.7158 (t0) cc_final: 0.6663 (p0) REVERT: A 406 ASP cc_start: 0.6867 (p0) cc_final: 0.6627 (p0) REVERT: A 426 ILE cc_start: 0.7907 (mm) cc_final: 0.7495 (tp) REVERT: A 464 TYR cc_start: 0.6512 (p90) cc_final: 0.5673 (p90) REVERT: A 498 PHE cc_start: 0.6910 (t80) cc_final: 0.6260 (t80) REVERT: A 509 MET cc_start: 0.7336 (tpt) cc_final: 0.7127 (tpt) REVERT: A 510 TRP cc_start: 0.7423 (p90) cc_final: 0.6845 (p90) REVERT: A 511 ILE cc_start: 0.7604 (mm) cc_final: 0.7322 (tp) REVERT: A 561 PHE cc_start: 0.7266 (t80) cc_final: 0.7053 (t80) REVERT: A 605 TYR cc_start: 0.8019 (m-80) cc_final: 0.7678 (m-80) REVERT: A 617 LEU cc_start: 0.6916 (mt) cc_final: 0.6029 (pt) REVERT: A 619 TYR cc_start: 0.7037 (m-80) cc_final: 0.6651 (m-80) REVERT: A 655 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6311 (pp20) REVERT: A 725 PHE cc_start: 0.6751 (m-80) cc_final: 0.6498 (m-80) REVERT: A 753 ILE cc_start: 0.7851 (mm) cc_final: 0.7523 (tp) REVERT: A 767 TYR cc_start: 0.6699 (p90) cc_final: 0.6317 (p90) REVERT: B 405 TYR cc_start: 0.5852 (p90) cc_final: 0.5172 (p90) REVERT: B 502 PHE cc_start: 0.5690 (m-80) cc_final: 0.5327 (m-10) REVERT: B 521 ASP cc_start: 0.7016 (p0) cc_final: 0.6327 (m-30) REVERT: B 548 ASN cc_start: 0.7730 (m-40) cc_final: 0.7424 (t0) REVERT: B 553 LYS cc_start: 0.8027 (tppt) cc_final: 0.7640 (tptp) REVERT: B 572 TYR cc_start: 0.6257 (p90) cc_final: 0.6036 (p90) REVERT: B 647 MET cc_start: 0.6449 (mmm) cc_final: 0.4599 (tmm) REVERT: B 771 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7058 (tp30) REVERT: B 777 GLU cc_start: 0.8081 (mp0) cc_final: 0.7849 (mp0) REVERT: B 782 LYS cc_start: 0.7294 (mtmm) cc_final: 0.6789 (mtmm) REVERT: B 814 MET cc_start: 0.4627 (mpp) cc_final: 0.4221 (mpp) REVERT: C 8 ASP cc_start: 0.8180 (p0) cc_final: 0.7374 (p0) REVERT: C 11 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7959 (mtmm) REVERT: C 53 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7344 (ptmt) REVERT: C 55 ASP cc_start: 0.7303 (t70) cc_final: 0.6982 (t0) REVERT: C 58 LEU cc_start: 0.8376 (mt) cc_final: 0.7982 (mt) REVERT: C 81 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7086 (mm-30) REVERT: C 82 ASN cc_start: 0.7836 (m110) cc_final: 0.7625 (m110) REVERT: C 84 ARG cc_start: 0.8344 (mtp180) cc_final: 0.6975 (ttm-80) REVERT: C 85 ASP cc_start: 0.8053 (m-30) cc_final: 0.7689 (m-30) REVERT: C 86 LEU cc_start: 0.8434 (mm) cc_final: 0.8226 (mm) REVERT: C 87 LEU cc_start: 0.8512 (pp) cc_final: 0.8242 (pp) REVERT: C 88 HIS cc_start: 0.7927 (m170) cc_final: 0.7073 (m90) REVERT: C 111 ASP cc_start: 0.7604 (t0) cc_final: 0.7306 (m-30) REVERT: C 117 SER cc_start: 0.7321 (t) cc_final: 0.6926 (m) REVERT: C 120 SER cc_start: 0.8669 (m) cc_final: 0.8395 (p) REVERT: C 132 SER cc_start: 0.7785 (p) cc_final: 0.7537 (p) REVERT: D 160 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7064 (tp40) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2336 time to fit residues: 95.6059 Evaluate side-chains 271 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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: 0.7980 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 105 optimal weight: 0.6980 chunk 122 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.168010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.133292 restraints weight = 32414.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.137765 restraints weight = 19588.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.140716 restraints weight = 13491.852| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10482 Z= 0.194 Angle : 0.651 12.057 14277 Z= 0.336 Chirality : 0.046 0.297 1636 Planarity : 0.005 0.051 1792 Dihedral : 5.228 31.999 1382 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 (0.23), residues: 1273 helix: 0.67 (0.35), residues: 223 sheet: 0.04 (0.24), residues: 472 loop : -0.57 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 447 HIS 0.005 0.001 HIS B 584 PHE 0.020 0.002 PHE B 568 TYR 0.022 0.001 TYR C 61 ARG 0.010 0.001 ARG B 512 *********************** 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 301 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7890 (mp) cc_final: 0.7569 (tp) REVERT: A 370 LEU cc_start: 0.8111 (mt) cc_final: 0.7865 (mt) REVERT: A 372 GLU cc_start: 0.6609 (tm-30) cc_final: 0.6371 (tm-30) REVERT: A 393 ASN cc_start: 0.7129 (t0) cc_final: 0.5978 (p0) REVERT: A 442 LYS cc_start: 0.6237 (tppt) cc_final: 0.5989 (tptt) REVERT: A 464 TYR cc_start: 0.6618 (p90) cc_final: 0.5662 (p90) REVERT: A 480 THR cc_start: 0.6828 (m) cc_final: 0.6214 (m) REVERT: A 489 GLN cc_start: 0.7664 (mp10) cc_final: 0.7367 (mp-120) REVERT: A 494 TYR cc_start: 0.5569 (m-80) cc_final: 0.5317 (m-80) REVERT: A 498 PHE cc_start: 0.6335 (t80) cc_final: 0.6133 (t80) REVERT: A 508 THR cc_start: 0.7803 (p) cc_final: 0.7386 (p) REVERT: A 509 MET cc_start: 0.7314 (tpt) cc_final: 0.7109 (tpt) REVERT: A 510 TRP cc_start: 0.7463 (p90) cc_final: 0.6816 (p90) REVERT: A 569 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6795 (tp40) REVERT: A 577 LYS cc_start: 0.8188 (mppt) cc_final: 0.7785 (mtmm) REVERT: A 580 GLN cc_start: 0.8389 (mp10) cc_final: 0.7759 (mp10) REVERT: A 605 TYR cc_start: 0.8009 (m-80) cc_final: 0.7743 (m-80) REVERT: A 619 TYR cc_start: 0.7019 (m-80) cc_final: 0.6719 (m-80) REVERT: A 655 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6366 (pp20) REVERT: A 725 PHE cc_start: 0.6756 (m-80) cc_final: 0.6516 (m-80) REVERT: A 733 MET cc_start: 0.3998 (ttt) cc_final: 0.3776 (ttt) REVERT: A 753 ILE cc_start: 0.7924 (mm) cc_final: 0.7671 (tp) REVERT: A 767 TYR cc_start: 0.6670 (p90) cc_final: 0.6274 (p90) REVERT: B 405 TYR cc_start: 0.5824 (p90) cc_final: 0.5105 (p90) REVERT: B 426 ILE cc_start: 0.4564 (tp) cc_final: 0.4140 (mm) REVERT: B 437 ASP cc_start: 0.8389 (t0) cc_final: 0.8179 (t0) REVERT: B 439 TYR cc_start: 0.7776 (m-10) cc_final: 0.7576 (m-10) REVERT: B 447 TRP cc_start: 0.6457 (p-90) cc_final: 0.6055 (p-90) REVERT: B 499 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 502 PHE cc_start: 0.5643 (m-80) cc_final: 0.5194 (m-10) REVERT: B 521 ASP cc_start: 0.7157 (p0) cc_final: 0.6378 (m-30) REVERT: B 553 LYS cc_start: 0.8046 (tppt) cc_final: 0.7647 (tptp) REVERT: B 554 VAL cc_start: 0.8157 (t) cc_final: 0.7786 (t) REVERT: B 556 TRP cc_start: 0.6618 (p90) cc_final: 0.6376 (p90) REVERT: B 647 MET cc_start: 0.6449 (mmm) cc_final: 0.4577 (tmm) REVERT: B 761 ASP cc_start: 0.6987 (t0) cc_final: 0.6710 (p0) REVERT: B 771 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7090 (tp30) REVERT: B 777 GLU cc_start: 0.8087 (mp0) cc_final: 0.7774 (mp0) REVERT: B 782 LYS cc_start: 0.7222 (mtmm) cc_final: 0.6850 (mtmm) REVERT: B 791 LYS cc_start: 0.5798 (tmtt) cc_final: 0.5457 (tptp) REVERT: B 814 MET cc_start: 0.4770 (mpp) cc_final: 0.4370 (mpp) REVERT: C 7 GLN cc_start: 0.7941 (pp30) cc_final: 0.7095 (pp30) REVERT: C 8 ASP cc_start: 0.8173 (p0) cc_final: 0.7153 (p0) REVERT: C 11 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7850 (mtmm) REVERT: C 13 LEU cc_start: 0.7833 (mt) cc_final: 0.7626 (mt) REVERT: C 53 LYS cc_start: 0.7510 (mtmt) cc_final: 0.7133 (ptmt) REVERT: C 62 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7642 (tt0) REVERT: C 65 LEU cc_start: 0.8322 (mt) cc_final: 0.8094 (mt) REVERT: C 75 GLN cc_start: 0.8230 (tt0) cc_final: 0.7344 (tp40) REVERT: C 81 GLU cc_start: 0.7931 (mm-30) cc_final: 0.6893 (mm-30) REVERT: C 82 ASN cc_start: 0.7867 (m110) cc_final: 0.7506 (m110) REVERT: C 84 ARG cc_start: 0.8270 (mtp180) cc_final: 0.6941 (ttm-80) REVERT: C 85 ASP cc_start: 0.7994 (m-30) cc_final: 0.7662 (m-30) REVERT: C 88 HIS cc_start: 0.7843 (m170) cc_final: 0.7134 (m90) REVERT: C 117 SER cc_start: 0.7221 (t) cc_final: 0.6974 (m) REVERT: C 120 SER cc_start: 0.8686 (m) cc_final: 0.8359 (p) REVERT: C 132 SER cc_start: 0.7664 (p) cc_final: 0.7423 (p) REVERT: C 133 LEU cc_start: 0.8389 (mt) cc_final: 0.8141 (mt) REVERT: C 134 GLN cc_start: 0.7991 (mp-120) cc_final: 0.7453 (mp10) REVERT: D 160 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7046 (tp40) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2468 time to fit residues: 101.5485 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 : 1.104 ------------------------------------------------------------------------------- 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: 0.3980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 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 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.165434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.131684 restraints weight = 32146.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.135954 restraints weight = 19574.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.138831 restraints weight = 13559.159| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10482 Z= 0.230 Angle : 0.674 10.034 14277 Z= 0.351 Chirality : 0.046 0.237 1636 Planarity : 0.005 0.052 1792 Dihedral : 5.353 25.968 1382 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -0.39 (0.23), residues: 1273 helix: 0.48 (0.35), residues: 224 sheet: -0.14 (0.24), residues: 478 loop : -0.54 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 447 HIS 0.006 0.001 HIS B 349 PHE 0.014 0.002 PHE B 568 TYR 0.015 0.001 TYR B 494 ARG 0.016 0.001 ARG A 400 *********************** 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 306 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.8007 (mp) cc_final: 0.7583 (tp) REVERT: A 372 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6524 (tm-30) REVERT: A 393 ASN cc_start: 0.6906 (t0) cc_final: 0.6320 (p0) REVERT: A 448 SER cc_start: 0.8937 (t) cc_final: 0.8613 (m) REVERT: A 464 TYR cc_start: 0.6653 (p90) cc_final: 0.5565 (p90) REVERT: A 480 THR cc_start: 0.6886 (m) cc_final: 0.6270 (m) REVERT: A 489 GLN cc_start: 0.7821 (mp10) cc_final: 0.7306 (mp10) REVERT: A 494 TYR cc_start: 0.5738 (m-10) cc_final: 0.5497 (m-80) REVERT: A 508 THR cc_start: 0.7583 (p) cc_final: 0.7137 (p) REVERT: A 509 MET cc_start: 0.7223 (tpt) cc_final: 0.7020 (tpt) REVERT: A 510 TRP cc_start: 0.7486 (p90) cc_final: 0.6929 (p90) REVERT: A 553 LYS cc_start: 0.6785 (tptt) cc_final: 0.6437 (tptt) REVERT: A 569 GLN cc_start: 0.6758 (tp-100) cc_final: 0.6490 (tp40) REVERT: A 577 LYS cc_start: 0.8140 (mppt) cc_final: 0.7741 (mtmm) REVERT: A 578 GLU cc_start: 0.7720 (pm20) cc_final: 0.7437 (pm20) REVERT: A 580 GLN cc_start: 0.8362 (mp10) cc_final: 0.7665 (mp10) REVERT: A 605 TYR cc_start: 0.8091 (m-80) cc_final: 0.7788 (m-10) REVERT: A 753 ILE cc_start: 0.7972 (mm) cc_final: 0.7719 (tp) REVERT: A 767 TYR cc_start: 0.6733 (p90) cc_final: 0.6337 (p90) REVERT: A 772 TRP cc_start: 0.7092 (p90) cc_final: 0.5794 (p90) REVERT: B 405 TYR cc_start: 0.5884 (p90) cc_final: 0.5094 (p90) REVERT: B 426 ILE cc_start: 0.4669 (tp) cc_final: 0.4201 (mm) REVERT: B 447 TRP cc_start: 0.6515 (p-90) cc_final: 0.6110 (p-90) REVERT: B 521 ASP cc_start: 0.7087 (p0) cc_final: 0.6381 (m-30) REVERT: B 553 LYS cc_start: 0.8046 (tppt) cc_final: 0.7646 (tptp) REVERT: B 567 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6907 (tm-30) REVERT: B 647 MET cc_start: 0.6467 (mmm) cc_final: 0.4487 (tmm) REVERT: B 771 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7297 (tp30) REVERT: B 777 GLU cc_start: 0.8171 (mp0) cc_final: 0.7741 (mp0) REVERT: B 782 LYS cc_start: 0.7226 (mtmm) cc_final: 0.6777 (mtmm) REVERT: B 791 LYS cc_start: 0.5876 (tmtt) cc_final: 0.5425 (tptp) REVERT: B 795 ILE cc_start: 0.8366 (mp) cc_final: 0.8135 (mp) REVERT: B 814 MET cc_start: 0.4736 (mpp) cc_final: 0.4396 (mpp) REVERT: C 7 GLN cc_start: 0.7947 (pp30) cc_final: 0.7149 (pp30) REVERT: C 8 ASP cc_start: 0.8130 (p0) cc_final: 0.7017 (p0) REVERT: C 11 LYS cc_start: 0.8409 (mtmm) cc_final: 0.7850 (mtmm) REVERT: C 53 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7347 (ptmt) REVERT: C 55 ASP cc_start: 0.7443 (t70) cc_final: 0.7073 (t0) REVERT: C 61 TYR cc_start: 0.7493 (m-80) cc_final: 0.7236 (m-80) REVERT: C 62 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7740 (tt0) REVERT: C 75 GLN cc_start: 0.8298 (tt0) cc_final: 0.7945 (tp40) REVERT: C 81 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7015 (mm-30) REVERT: C 82 ASN cc_start: 0.7937 (m110) cc_final: 0.7500 (m110) REVERT: C 84 ARG cc_start: 0.8361 (mtp180) cc_final: 0.7057 (ttm-80) REVERT: C 85 ASP cc_start: 0.8046 (m-30) cc_final: 0.7721 (m-30) REVERT: C 88 HIS cc_start: 0.7825 (m170) cc_final: 0.7145 (m90) REVERT: C 117 SER cc_start: 0.7342 (t) cc_final: 0.7039 (m) REVERT: C 134 GLN cc_start: 0.7975 (mp-120) cc_final: 0.7698 (mp-120) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2431 time to fit residues: 101.5819 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 : 1.226 ------------------------------------------------------------------------------- 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: 0.6980 chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.163868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.130631 restraints weight = 32197.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.134901 restraints weight = 19471.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.137624 restraints weight = 13461.627| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10482 Z= 0.261 Angle : 0.715 10.885 14277 Z= 0.376 Chirality : 0.047 0.185 1636 Planarity : 0.005 0.053 1792 Dihedral : 5.605 32.184 1382 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.69 (0.23), residues: 1273 helix: 0.18 (0.34), residues: 221 sheet: -0.27 (0.24), residues: 469 loop : -0.75 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 447 HIS 0.006 0.001 HIS B 349 PHE 0.018 0.002 PHE C 92 TYR 0.016 0.002 TYR B 763 ARG 0.006 0.001 ARG A 400 *********************** 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 294 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7957 (mp) cc_final: 0.7585 (tp) REVERT: A 339 LEU cc_start: 0.8126 (mm) cc_final: 0.7779 (mm) REVERT: A 373 LYS cc_start: 0.8373 (tmmt) cc_final: 0.8107 (tptp) REVERT: A 393 ASN cc_start: 0.6872 (t0) cc_final: 0.6288 (p0) REVERT: A 426 ILE cc_start: 0.7803 (mp) cc_final: 0.7366 (tp) REVERT: A 464 TYR cc_start: 0.6786 (p90) cc_final: 0.5828 (p90) REVERT: A 493 PHE cc_start: 0.7980 (m-80) cc_final: 0.7289 (m-80) REVERT: A 509 MET cc_start: 0.7260 (tpt) cc_final: 0.6996 (tpt) REVERT: A 510 TRP cc_start: 0.7485 (p90) cc_final: 0.7084 (p90) REVERT: A 569 GLN cc_start: 0.6786 (tp-100) cc_final: 0.6504 (tp40) REVERT: A 577 LYS cc_start: 0.8108 (mppt) cc_final: 0.7731 (mtmm) REVERT: A 753 ILE cc_start: 0.7962 (mm) cc_final: 0.7631 (tp) REVERT: A 767 TYR cc_start: 0.6758 (p90) cc_final: 0.6373 (p90) REVERT: A 789 ASN cc_start: 0.8037 (p0) cc_final: 0.7831 (p0) REVERT: A 823 ILE cc_start: 0.7147 (mt) cc_final: 0.6936 (pt) REVERT: B 405 TYR cc_start: 0.5846 (p90) cc_final: 0.5067 (p90) REVERT: B 426 ILE cc_start: 0.4789 (tp) cc_final: 0.4344 (mm) REVERT: B 427 ASP cc_start: 0.6720 (t70) cc_final: 0.6463 (t0) REVERT: B 443 MET cc_start: 0.6633 (tpp) cc_final: 0.6279 (tpp) REVERT: B 447 TRP cc_start: 0.6650 (p-90) cc_final: 0.6136 (p-90) REVERT: B 478 HIS cc_start: 0.6542 (t-90) cc_final: 0.6183 (t-90) REVERT: B 493 PHE cc_start: 0.8060 (m-80) cc_final: 0.7851 (m-80) REVERT: B 512 ARG cc_start: 0.6696 (pmt-80) cc_final: 0.6130 (pmt-80) REVERT: B 530 ASP cc_start: 0.8320 (m-30) cc_final: 0.8042 (m-30) REVERT: B 544 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6409 (tp30) REVERT: B 545 ILE cc_start: 0.6578 (tp) cc_final: 0.6164 (tp) REVERT: B 553 LYS cc_start: 0.8082 (tppt) cc_final: 0.7741 (tptp) REVERT: B 567 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 638 MET cc_start: 0.6033 (ppp) cc_final: 0.5829 (ppp) REVERT: B 647 MET cc_start: 0.6448 (mmm) cc_final: 0.4552 (tmm) REVERT: B 660 LEU cc_start: 0.7874 (tp) cc_final: 0.7452 (tp) REVERT: B 698 ASN cc_start: 0.6681 (p0) cc_final: 0.6358 (t0) REVERT: B 771 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7364 (tp30) REVERT: B 777 GLU cc_start: 0.8167 (mp0) cc_final: 0.7762 (mp0) REVERT: B 782 LYS cc_start: 0.7256 (mtmm) cc_final: 0.6710 (mtmm) REVERT: B 795 ILE cc_start: 0.8346 (mp) cc_final: 0.8145 (mp) REVERT: B 814 MET cc_start: 0.4822 (mpp) cc_final: 0.4452 (mpp) REVERT: C 7 GLN cc_start: 0.7943 (pp30) cc_final: 0.7041 (pp30) REVERT: C 8 ASP cc_start: 0.8037 (p0) cc_final: 0.6897 (p0) REVERT: C 11 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7790 (mtmm) REVERT: C 53 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7408 (ptmt) REVERT: C 55 ASP cc_start: 0.7415 (t70) cc_final: 0.7138 (t70) REVERT: C 62 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7689 (tt0) REVERT: C 65 LEU cc_start: 0.8344 (mt) cc_final: 0.8132 (mt) REVERT: C 75 GLN cc_start: 0.8328 (tt0) cc_final: 0.7962 (tp-100) REVERT: C 81 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7082 (mm-30) REVERT: C 84 ARG cc_start: 0.8390 (mtp180) cc_final: 0.7228 (ttm-80) REVERT: C 85 ASP cc_start: 0.8146 (m-30) cc_final: 0.7767 (m-30) REVERT: C 87 LEU cc_start: 0.8630 (pp) cc_final: 0.8406 (pp) REVERT: C 88 HIS cc_start: 0.7914 (m170) cc_final: 0.7351 (m90) REVERT: C 117 SER cc_start: 0.7410 (t) cc_final: 0.7078 (m) REVERT: C 133 LEU cc_start: 0.8357 (mt) cc_final: 0.8129 (mt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2583 time to fit residues: 102.7535 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 : 1.889 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 22 optimal weight: 0.0980 chunk 75 optimal weight: 0.0020 chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 489 GLN A 796 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.166715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.133118 restraints weight = 31686.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.137459 restraints weight = 19205.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.140345 restraints weight = 13249.549| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 10482 Z= 0.207 Angle : 0.708 17.454 14277 Z= 0.364 Chirality : 0.047 0.265 1636 Planarity : 0.005 0.061 1792 Dihedral : 5.252 24.171 1382 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % 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: -0.45 (0.23), residues: 1273 helix: 0.42 (0.35), residues: 223 sheet: -0.14 (0.24), residues: 478 loop : -0.60 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 447 HIS 0.003 0.001 HIS B 685 PHE 0.017 0.001 PHE B 568 TYR 0.021 0.001 TYR C 61 ARG 0.013 0.001 ARG A 446 *********************** 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 298 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 1.183 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: 0.7964 (mp) cc_final: 0.7569 (tp) REVERT: A 372 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6269 (tm-30) REVERT: A 373 LYS cc_start: 0.8291 (tmmt) cc_final: 0.8090 (tptp) REVERT: A 426 ILE cc_start: 0.7761 (mp) cc_final: 0.7317 (tp) REVERT: A 446 ARG cc_start: 0.7289 (tpp80) cc_final: 0.7084 (tpp80) REVERT: A 450 SER cc_start: 0.7412 (t) cc_final: 0.7186 (m) REVERT: A 464 TYR cc_start: 0.6802 (p90) cc_final: 0.5805 (p90) REVERT: A 484 LYS cc_start: 0.7397 (tptt) cc_final: 0.6590 (tmtt) REVERT: A 485 ASN cc_start: 0.6471 (t0) cc_final: 0.6008 (t0) REVERT: A 489 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: A 493 PHE cc_start: 0.7848 (m-80) cc_final: 0.7448 (m-80) REVERT: A 498 PHE cc_start: 0.7069 (t80) cc_final: 0.6729 (t80) REVERT: A 508 THR cc_start: 0.7583 (p) cc_final: 0.7017 (p) REVERT: A 510 TRP cc_start: 0.7398 (p90) cc_final: 0.6806 (p90) REVERT: A 540 ASN cc_start: 0.8128 (t0) cc_final: 0.7672 (t0) REVERT: A 553 LYS cc_start: 0.6823 (tptt) cc_final: 0.6504 (tptt) REVERT: A 569 GLN cc_start: 0.6722 (tp-100) cc_final: 0.6468 (tp40) REVERT: A 577 LYS cc_start: 0.7972 (mppt) cc_final: 0.7636 (mtmm) REVERT: A 580 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8192 (mm-40) REVERT: A 632 MET cc_start: 0.1257 (mmm) cc_final: 0.0253 (mmm) REVERT: A 753 ILE cc_start: 0.7864 (mm) cc_final: 0.7612 (tp) REVERT: A 767 TYR cc_start: 0.6730 (p90) cc_final: 0.6331 (p90) REVERT: A 772 TRP cc_start: 0.7174 (p90) cc_final: 0.6906 (p90) REVERT: B 405 TYR cc_start: 0.5876 (p90) cc_final: 0.5091 (p90) REVERT: B 478 HIS cc_start: 0.6485 (t-90) cc_final: 0.6146 (t-90) REVERT: B 502 PHE cc_start: 0.5960 (m-80) cc_final: 0.5197 (m-80) REVERT: B 521 ASP cc_start: 0.7125 (p0) cc_final: 0.6407 (m-30) REVERT: B 530 ASP cc_start: 0.8424 (m-30) cc_final: 0.8140 (m-30) REVERT: B 544 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6341 (tp30) REVERT: B 545 ILE cc_start: 0.6549 (tp) cc_final: 0.6084 (tp) REVERT: B 553 LYS cc_start: 0.8122 (tppt) cc_final: 0.7829 (tptp) REVERT: B 567 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6912 (tm-30) REVERT: B 638 MET cc_start: 0.6087 (ppp) cc_final: 0.5866 (ppp) REVERT: B 639 ARG cc_start: 0.6963 (mmp80) cc_final: 0.6658 (mmp80) REVERT: B 647 MET cc_start: 0.6350 (mmm) cc_final: 0.4459 (tmm) REVERT: B 660 LEU cc_start: 0.7872 (tp) cc_final: 0.7413 (tp) REVERT: B 698 ASN cc_start: 0.6710 (p0) cc_final: 0.6441 (t0) REVERT: B 771 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7324 (tp30) REVERT: B 782 LYS cc_start: 0.7288 (mtmm) cc_final: 0.6957 (mtmm) REVERT: B 814 MET cc_start: 0.4558 (mpp) cc_final: 0.4237 (mpp) REVERT: C 8 ASP cc_start: 0.7953 (p0) cc_final: 0.6806 (p0) REVERT: C 11 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7744 (mtmm) REVERT: C 53 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7475 (ptmt) REVERT: C 54 MET cc_start: 0.8270 (mtm) cc_final: 0.8005 (mtt) REVERT: C 55 ASP cc_start: 0.7389 (t70) cc_final: 0.7149 (t70) REVERT: C 61 TYR cc_start: 0.7467 (m-80) cc_final: 0.7233 (m-80) REVERT: C 65 LEU cc_start: 0.8296 (mt) cc_final: 0.8028 (mt) REVERT: C 75 GLN cc_start: 0.8297 (tt0) cc_final: 0.7892 (tp40) REVERT: C 81 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7161 (mm-30) REVERT: C 85 ASP cc_start: 0.8122 (m-30) cc_final: 0.7694 (m-30) REVERT: C 87 LEU cc_start: 0.8558 (pp) cc_final: 0.8356 (pp) REVERT: C 88 HIS cc_start: 0.7767 (m170) cc_final: 0.7384 (m90) REVERT: C 117 SER cc_start: 0.7463 (t) cc_final: 0.6982 (m) REVERT: C 133 LEU cc_start: 0.8265 (mt) cc_final: 0.8055 (mt) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.2511 time to fit residues: 101.4755 Evaluate side-chains 279 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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: 0.1980 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.165571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.131727 restraints weight = 31680.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.136016 restraints weight = 19292.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.138898 restraints weight = 13402.145| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.8112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10482 Z= 0.222 Angle : 0.713 15.544 14277 Z= 0.366 Chirality : 0.047 0.215 1636 Planarity : 0.005 0.084 1792 Dihedral : 5.338 23.849 1382 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.37 % 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: -0.46 (0.24), residues: 1273 helix: 0.37 (0.34), residues: 223 sheet: -0.16 (0.24), residues: 482 loop : -0.58 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 447 HIS 0.004 0.001 HIS B 349 PHE 0.019 0.002 PHE C 92 TYR 0.018 0.001 TYR A 572 ARG 0.010 0.001 ARG A 446 ********************** 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 297 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.076 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 339 LEU cc_start: 0.8111 (mm) cc_final: 0.7802 (mm) REVERT: A 372 GLU cc_start: 0.6471 (tm-30) cc_final: 0.6225 (tm-30) REVERT: A 426 ILE cc_start: 0.7803 (mp) cc_final: 0.7314 (tp) REVERT: A 464 TYR cc_start: 0.6880 (p90) cc_final: 0.6084 (p90) REVERT: A 465 HIS cc_start: 0.6745 (t-90) cc_final: 0.6512 (t-90) REVERT: A 489 GLN cc_start: 0.7873 (mp-120) cc_final: 0.7606 (mp10) REVERT: A 493 PHE cc_start: 0.7891 (m-80) cc_final: 0.7489 (m-80) REVERT: A 498 PHE cc_start: 0.7061 (t80) cc_final: 0.6655 (t80) REVERT: A 510 TRP cc_start: 0.7255 (p90) cc_final: 0.6817 (p90) REVERT: A 569 GLN cc_start: 0.6710 (tp-100) cc_final: 0.6451 (tp40) REVERT: A 577 LYS cc_start: 0.7894 (mppt) cc_final: 0.7518 (mtmm) REVERT: A 580 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8226 (mm-40) REVERT: A 597 LEU cc_start: 0.7978 (tp) cc_final: 0.7682 (tt) REVERT: A 632 MET cc_start: 0.1400 (mmm) cc_final: 0.0488 (mmm) REVERT: A 663 LYS cc_start: 0.7509 (mtpt) cc_final: 0.7303 (mtpt) REVERT: A 753 ILE cc_start: 0.7879 (mm) cc_final: 0.7628 (tp) REVERT: A 767 TYR cc_start: 0.6760 (p90) cc_final: 0.6326 (p90) REVERT: B 405 TYR cc_start: 0.5903 (p90) cc_final: 0.5115 (p90) REVERT: B 426 ILE cc_start: 0.4679 (tp) cc_final: 0.4240 (mm) REVERT: B 447 TRP cc_start: 0.6466 (p-90) cc_final: 0.6220 (p-90) REVERT: B 478 HIS cc_start: 0.6420 (t-90) cc_final: 0.6115 (t-90) REVERT: B 502 PHE cc_start: 0.6068 (m-80) cc_final: 0.5393 (m-80) REVERT: B 530 ASP cc_start: 0.8377 (m-30) cc_final: 0.8026 (m-30) REVERT: B 544 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6262 (tp30) REVERT: B 545 ILE cc_start: 0.6604 (tp) cc_final: 0.6142 (tp) REVERT: B 553 LYS cc_start: 0.8110 (tppt) cc_final: 0.7789 (tptp) REVERT: B 591 SER cc_start: 0.8530 (p) cc_final: 0.8330 (p) REVERT: B 638 MET cc_start: 0.6137 (ppp) cc_final: 0.5909 (ppp) REVERT: B 639 ARG cc_start: 0.7054 (mmp80) cc_final: 0.6726 (mmp80) REVERT: B 647 MET cc_start: 0.6475 (mmm) cc_final: 0.4601 (tmm) REVERT: B 660 LEU cc_start: 0.7914 (tp) cc_final: 0.7707 (tp) REVERT: B 698 ASN cc_start: 0.6674 (p0) cc_final: 0.6424 (t0) REVERT: B 701 PHE cc_start: 0.5883 (p90) cc_final: 0.5665 (p90) REVERT: B 733 MET cc_start: 0.5341 (ptm) cc_final: 0.4633 (tmm) REVERT: B 771 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7141 (tp30) REVERT: B 781 MET cc_start: 0.7851 (tmm) cc_final: 0.7643 (tmm) REVERT: B 782 LYS cc_start: 0.7259 (mtmm) cc_final: 0.6658 (mtmm) REVERT: B 791 LYS cc_start: 0.6261 (mmmt) cc_final: 0.6021 (mmmt) REVERT: B 814 MET cc_start: 0.4608 (mpp) cc_final: 0.4320 (mpp) REVERT: C 7 GLN cc_start: 0.7874 (pp30) cc_final: 0.7079 (pp30) REVERT: C 8 ASP cc_start: 0.7948 (p0) cc_final: 0.6830 (p0) REVERT: C 11 LYS cc_start: 0.8392 (mtmm) cc_final: 0.7749 (mtmm) REVERT: C 51 LEU cc_start: 0.7468 (mt) cc_final: 0.7224 (pp) REVERT: C 54 MET cc_start: 0.8245 (mtm) cc_final: 0.7993 (mmt) REVERT: C 55 ASP cc_start: 0.7403 (t70) cc_final: 0.7176 (t0) REVERT: C 65 LEU cc_start: 0.8280 (mt) cc_final: 0.8053 (mt) REVERT: C 75 GLN cc_start: 0.8361 (tt0) cc_final: 0.7909 (tp-100) REVERT: C 81 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7154 (mm-30) REVERT: C 85 ASP cc_start: 0.8179 (m-30) cc_final: 0.7730 (m-30) REVERT: C 88 HIS cc_start: 0.7827 (m170) cc_final: 0.7576 (m90) REVERT: C 117 SER cc_start: 0.7367 (t) cc_final: 0.6823 (m) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2411 time to fit residues: 98.2676 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 : 1.066 ------------------------------------------------------------------------------- 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: 0.7980 chunk 66 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 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 = 0.4410 r_free = 0.4410 target = 0.163508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.129731 restraints weight = 31746.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.134068 restraints weight = 19219.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.136901 restraints weight = 13363.016| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.8548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10482 Z= 0.242 Angle : 0.726 15.438 14277 Z= 0.376 Chirality : 0.047 0.242 1636 Planarity : 0.006 0.098 1792 Dihedral : 5.646 35.281 1382 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.66 (0.23), residues: 1273 helix: 0.26 (0.34), residues: 223 sheet: -0.20 (0.25), residues: 459 loop : -0.80 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 556 HIS 0.004 0.001 HIS B 349 PHE 0.014 0.002 PHE B 793 TYR 0.021 0.002 TYR A 605 ARG 0.014 0.001 ARG A 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4347.58 seconds wall clock time: 78 minutes 37.96 seconds (4717.96 seconds total)