Starting phenix.real_space_refine on Wed Feb 12 09:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nph_0470/02_2025/6nph_0470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nph_0470/02_2025/6nph_0470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nph_0470/02_2025/6nph_0470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nph_0470/02_2025/6nph_0470.map" model { file = "/net/cci-nas-00/data/ceres_data/6nph_0470/02_2025/6nph_0470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nph_0470/02_2025/6nph_0470.cif" } resolution = 2.9 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= 0.013 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 7 5.49 5 S 46 5.16 5 Cl 4 4.86 5 C 5016 2.51 5 N 1119 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7504 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3567 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain: "B" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3567 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 159 Unusual residues: {' K': 1, ' CL': 2, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 211 Unusual residues: {' K': 1, ' CL': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.48, per 1000 atoms: 0.33 Number of scatterers: 7504 At special positions: 0 Unit cell: (105.5, 77.015, 90.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 46 16.00 P 7 15.00 O 1310 8.00 N 1119 7.00 C 5016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 507 " 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: 1.91 Conformation dependent library (CDL) restraints added in 961.9 milliseconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 70.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 238 through 265 Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.973A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 320 removed outlier: 3.741A pdb=" N SER A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.580A pdb=" N ILE A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 349 through 375 removed outlier: 3.919A pdb=" N GLU A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.552A pdb=" N ALA A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY A 425 " --> pdb=" O ILE A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 425' Processing helix chain 'A' and resid 434 through 463 Proline residue: A 440 - end of helix removed outlier: 3.691A pdb=" N LEU A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 527 through 530 Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 561 through 566 removed outlier: 4.178A pdb=" N ALA A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 565 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.572A pdb=" N PHE A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 625 Proline residue: A 601 - end of helix removed outlier: 3.511A pdb=" N ASN A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 3.587A pdb=" N ASN A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 676 removed outlier: 3.646A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 238 through 265 Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.973A pdb=" N LEU B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 320 removed outlier: 3.743A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.581A pdb=" N ILE B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 Processing helix chain 'B' and resid 349 through 375 removed outlier: 3.920A pdb=" N GLU B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 398 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.551A pdb=" N ALA B 424 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY B 425 " --> pdb=" O ILE B 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 421 through 425' Processing helix chain 'B' and resid 434 through 463 Proline residue: B 440 - end of helix removed outlier: 3.692A pdb=" N LEU B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 527 through 530 Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 561 through 566 removed outlier: 4.177A pdb=" N ALA B 564 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 592 removed outlier: 3.573A pdb=" N PHE B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 625 Proline residue: B 601 - end of helix removed outlier: 3.511A pdb=" N ASN B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.587A pdb=" N ASN B 656 " --> pdb=" O MET B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 676 removed outlier: 3.645A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1272 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: 2.12 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1108 1.31 - 1.43: 2113 1.43 - 1.56: 4241 1.56 - 1.69: 124 1.69 - 1.82: 77 Bond restraints: 7663 Sorted by residual: bond pdb=" C31 POV A 702 " pdb=" O31 POV A 702 " ideal model delta sigma weight residual 1.327 1.438 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.436 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C31 POV B 802 " pdb=" O31 POV B 802 " ideal model delta sigma weight residual 1.327 1.432 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C31 POV B 801 " pdb=" O31 POV B 801 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C21 POV A 703 " pdb=" O21 POV A 703 " ideal model delta sigma weight residual 1.330 1.433 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 7658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.22: 10278 6.22 - 12.44: 65 12.44 - 18.67: 2 18.67 - 24.89: 2 24.89 - 31.11: 4 Bond angle restraints: 10351 Sorted by residual: angle pdb=" C12 POV A 703 " pdb=" N POV A 703 " pdb=" C15 POV A 703 " ideal model delta sigma weight residual 112.10 80.99 31.11 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C13 POV A 703 " pdb=" N POV A 703 " pdb=" C14 POV A 703 " ideal model delta sigma weight residual 108.80 79.67 29.13 3.00e+00 1.11e-01 9.43e+01 angle pdb=" C13 POV A 703 " pdb=" N POV A 703 " pdb=" C15 POV A 703 " ideal model delta sigma weight residual 109.35 80.29 29.06 3.00e+00 1.11e-01 9.38e+01 angle pdb=" C12 POV A 703 " pdb=" N POV A 703 " pdb=" C14 POV A 703 " ideal model delta sigma weight residual 107.13 80.42 26.71 3.00e+00 1.11e-01 7.93e+01 angle pdb=" C14 POV A 703 " pdb=" N POV A 703 " pdb=" C15 POV A 703 " ideal model delta sigma weight residual 108.02 132.52 -24.50 3.00e+00 1.11e-01 6.67e+01 ... (remaining 10346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.94: 4223 28.94 - 57.87: 210 57.87 - 86.81: 34 86.81 - 115.75: 5 115.75 - 144.68: 5 Dihedral angle restraints: 4477 sinusoidal: 1791 harmonic: 2686 Sorted by residual: dihedral pdb=" CD ARG A 630 " pdb=" NE ARG A 630 " pdb=" CZ ARG A 630 " pdb=" NH1 ARG A 630 " ideal model delta sinusoidal sigma weight residual 0.00 -41.33 41.33 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CA ALA A 530 " pdb=" C ALA A 530 " pdb=" N GLY A 531 " pdb=" CA GLY A 531 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ALA B 530 " pdb=" C ALA B 530 " pdb=" N GLY B 531 " pdb=" CA GLY B 531 " ideal model delta harmonic sigma weight residual 180.00 155.88 24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 667 0.043 - 0.085: 360 0.085 - 0.128: 110 0.128 - 0.170: 33 0.170 - 0.213: 7 Chirality restraints: 1177 Sorted by residual: chirality pdb=" CA PHE B 387 " pdb=" N PHE B 387 " pdb=" C PHE B 387 " pdb=" CB PHE B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PHE A 387 " pdb=" N PHE A 387 " pdb=" C PHE A 387 " pdb=" CB PHE A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA SER A 525 " pdb=" N SER A 525 " pdb=" C SER A 525 " pdb=" CB SER A 525 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1174 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 630 " 0.719 9.50e-02 1.11e+02 3.22e-01 6.33e+01 pdb=" NE ARG A 630 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 630 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 630 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 630 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 630 " -0.309 9.50e-02 1.11e+02 1.39e-01 1.18e+01 pdb=" NE ARG B 630 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 630 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 630 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 630 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 416 " 0.047 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 417 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 417 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 417 " 0.039 5.00e-02 4.00e+02 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 2663 2.86 - 3.43: 7669 3.43 - 4.00: 13623 4.00 - 4.57: 20248 4.57 - 5.14: 29229 Nonbonded interactions: 73432 Sorted by model distance: nonbonded pdb=" OG SER B 474 " pdb=" O GLY B 490 " model vdw 2.292 3.040 nonbonded pdb=" OG SER A 474 " pdb=" O GLY A 490 " model vdw 2.292 3.040 nonbonded pdb=" O MET A 518 " pdb=" OG SER A 522 " model vdw 2.315 3.040 nonbonded pdb=" O MET B 518 " pdb=" OG SER B 522 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLN B 406 " pdb=" OG SER B 410 " model vdw 2.322 3.040 ... (remaining 73427 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' and (resid 206 through 677 or resid 701 through 703 or resid 706)) selection = (chain 'B' and (resid 206 through 677 or resid 801 through 803 or resid 806)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.740 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 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 : 0.012 0.111 7663 Z= 0.776 Angle : 1.415 31.111 10351 Z= 0.626 Chirality : 0.058 0.213 1177 Planarity : 0.012 0.322 1243 Dihedral : 18.336 144.683 2763 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.67 % Allowed : 7.73 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.20), residues: 940 helix: -2.32 (0.15), residues: 600 sheet: None (None), residues: 0 loop : -3.64 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 657 HIS 0.003 0.001 HIS A 512 PHE 0.032 0.003 PHE B 387 TYR 0.010 0.002 TYR B 491 ARG 0.004 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.753 Fit side-chains REVERT: A 525 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7876 (p) REVERT: A 568 LYS cc_start: 0.6795 (tttt) cc_final: 0.6162 (tmtm) REVERT: B 211 LYS cc_start: 0.7463 (tttm) cc_final: 0.6281 (mptt) REVERT: B 575 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7341 (pt0) outliers start: 35 outliers final: 6 residues processed: 213 average time/residue: 0.8704 time to fit residues: 199.7405 Evaluate side-chains 121 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.0010 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 298 ASN A 327 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN A 664 ASN B 298 ASN B 327 GLN B 357 GLN B 512 HIS B 664 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113520 restraints weight = 8452.887| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.84 r_work: 0.3190 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7663 Z= 0.192 Angle : 0.620 12.965 10351 Z= 0.315 Chirality : 0.043 0.161 1177 Planarity : 0.004 0.054 1243 Dihedral : 16.533 105.553 1309 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.47 % Allowed : 15.20 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 940 helix: -0.08 (0.20), residues: 620 sheet: None (None), residues: 0 loop : -3.22 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 209 HIS 0.003 0.001 HIS A 620 PHE 0.015 0.001 PHE A 415 TYR 0.015 0.001 TYR A 371 ARG 0.004 0.001 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.759 Fit side-chains REVERT: A 568 LYS cc_start: 0.7616 (tttt) cc_final: 0.6762 (tttm) REVERT: A 634 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8139 (ttmt) REVERT: B 304 MET cc_start: 0.9022 (ttp) cc_final: 0.8698 (ttp) REVERT: B 345 ILE cc_start: 0.8533 (mt) cc_final: 0.8263 (mp) REVERT: B 364 LEU cc_start: 0.7677 (tp) cc_final: 0.7417 (tt) REVERT: B 373 ILE cc_start: 0.8438 (pt) cc_final: 0.7941 (mt) REVERT: B 479 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5092 (mm) REVERT: B 524 PHE cc_start: 0.8020 (t80) cc_final: 0.7185 (t80) REVERT: B 549 LYS cc_start: 0.8151 (tptm) cc_final: 0.7733 (tppt) REVERT: B 575 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7496 (pt0) outliers start: 41 outliers final: 11 residues processed: 157 average time/residue: 0.8979 time to fit residues: 152.2959 Evaluate side-chains 122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 427 ASN A 436 GLN B 512 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111308 restraints weight = 8552.022| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.85 r_work: 0.3013 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7663 Z= 0.145 Angle : 0.517 7.474 10351 Z= 0.270 Chirality : 0.040 0.164 1177 Planarity : 0.003 0.042 1243 Dihedral : 15.757 106.706 1301 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.80 % Allowed : 19.60 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 940 helix: 0.95 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -3.09 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 209 HIS 0.002 0.001 HIS B 620 PHE 0.012 0.001 PHE A 387 TYR 0.008 0.001 TYR B 676 ARG 0.003 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.746 Fit side-chains REVERT: A 285 GLU cc_start: 0.8037 (pm20) cc_final: 0.7761 (pm20) REVERT: A 340 ILE cc_start: 0.8285 (pp) cc_final: 0.8060 (pt) REVERT: A 381 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8063 (t) REVERT: A 516 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8599 (tp-100) REVERT: A 568 LYS cc_start: 0.7616 (tttt) cc_final: 0.6989 (tttm) REVERT: A 570 TYR cc_start: 0.7988 (m-80) cc_final: 0.7566 (m-80) REVERT: B 304 MET cc_start: 0.9040 (ttp) cc_final: 0.8648 (ttp) REVERT: B 315 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6088 (mt-10) REVERT: B 345 ILE cc_start: 0.8229 (mt) cc_final: 0.7929 (mm) REVERT: B 373 ILE cc_start: 0.8457 (pt) cc_final: 0.8069 (mt) REVERT: B 377 ILE cc_start: 0.9110 (mt) cc_final: 0.8828 (mp) REVERT: B 575 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7531 (pt0) outliers start: 21 outliers final: 7 residues processed: 143 average time/residue: 0.7073 time to fit residues: 110.9394 Evaluate side-chains 120 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 0.0170 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 73 optimal weight: 8.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 512 HIS B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108767 restraints weight = 8603.358| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.89 r_work: 0.2961 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7663 Z= 0.148 Angle : 0.511 6.989 10351 Z= 0.265 Chirality : 0.041 0.172 1177 Planarity : 0.003 0.037 1243 Dihedral : 14.788 107.405 1301 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.07 % Allowed : 20.27 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 940 helix: 1.44 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.86 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 209 HIS 0.002 0.001 HIS A 512 PHE 0.013 0.001 PHE B 415 TYR 0.008 0.001 TYR B 676 ARG 0.004 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.759 Fit side-chains REVERT: A 285 GLU cc_start: 0.8166 (pm20) cc_final: 0.7964 (pm20) REVERT: A 324 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.5500 (ttt) REVERT: A 568 LYS cc_start: 0.7915 (tttt) cc_final: 0.7204 (tttm) REVERT: A 570 TYR cc_start: 0.8128 (m-80) cc_final: 0.7700 (m-80) REVERT: A 634 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: B 315 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: B 324 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6988 (pmm) REVERT: B 373 ILE cc_start: 0.8572 (pt) cc_final: 0.8356 (mt) REVERT: B 479 ILE cc_start: 0.5554 (OUTLIER) cc_final: 0.4934 (mm) REVERT: B 525 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7882 (t) REVERT: B 575 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7226 (pt0) REVERT: B 583 THR cc_start: 0.8662 (t) cc_final: 0.8386 (m) outliers start: 38 outliers final: 10 residues processed: 140 average time/residue: 0.7538 time to fit residues: 115.3003 Evaluate side-chains 118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN B 512 HIS B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105929 restraints weight = 8624.546| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.90 r_work: 0.2915 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7663 Z= 0.162 Angle : 0.508 7.677 10351 Z= 0.261 Chirality : 0.041 0.163 1177 Planarity : 0.003 0.037 1243 Dihedral : 14.388 107.125 1301 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.80 % Allowed : 22.13 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 940 helix: 1.64 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.79 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.014 0.001 PHE A 387 TYR 0.009 0.001 TYR B 676 ARG 0.002 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.755 Fit side-chains REVERT: A 225 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.6156 (mpt) REVERT: A 285 GLU cc_start: 0.8189 (pm20) cc_final: 0.7907 (pm20) REVERT: A 324 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.5695 (ttt) REVERT: A 381 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 568 LYS cc_start: 0.7999 (tttt) cc_final: 0.7285 (tttm) REVERT: A 570 TYR cc_start: 0.8149 (m-80) cc_final: 0.7644 (m-80) REVERT: B 211 LYS cc_start: 0.9098 (tttm) cc_final: 0.8850 (tttm) REVERT: B 280 ARG cc_start: 0.7555 (mpt90) cc_final: 0.7248 (mmt-90) REVERT: B 315 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6410 (mt-10) REVERT: B 322 LEU cc_start: 0.7863 (mm) cc_final: 0.7546 (mm) REVERT: B 324 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6924 (pmm) REVERT: B 479 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5115 (mm) REVERT: B 494 SER cc_start: 0.7075 (t) cc_final: 0.6798 (m) REVERT: B 525 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.8102 (p) REVERT: B 575 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7212 (pt0) REVERT: B 583 THR cc_start: 0.8660 (t) cc_final: 0.8401 (m) REVERT: B 677 LYS cc_start: 0.6423 (pttt) cc_final: 0.5945 (tttt) outliers start: 21 outliers final: 7 residues processed: 127 average time/residue: 0.8660 time to fit residues: 118.9508 Evaluate side-chains 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104770 restraints weight = 8608.376| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.90 r_work: 0.2885 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7663 Z= 0.170 Angle : 0.510 7.885 10351 Z= 0.263 Chirality : 0.041 0.164 1177 Planarity : 0.003 0.035 1243 Dihedral : 14.248 106.934 1301 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.87 % Allowed : 21.07 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 940 helix: 1.79 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.015 0.001 PHE A 387 TYR 0.009 0.001 TYR B 676 ARG 0.006 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.742 Fit side-chains REVERT: A 225 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.6133 (mpt) REVERT: A 285 GLU cc_start: 0.8338 (pm20) cc_final: 0.8099 (pm20) REVERT: A 315 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 324 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.5802 (ttt) REVERT: A 568 LYS cc_start: 0.8116 (tttt) cc_final: 0.7397 (tttm) REVERT: A 570 TYR cc_start: 0.8158 (m-80) cc_final: 0.7688 (m-80) REVERT: A 634 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8326 (ttmt) REVERT: B 211 LYS cc_start: 0.9100 (tttm) cc_final: 0.8835 (tttm) REVERT: B 280 ARG cc_start: 0.7346 (mpt90) cc_final: 0.6986 (mmt-90) REVERT: B 315 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: B 322 LEU cc_start: 0.7835 (mm) cc_final: 0.7553 (mm) REVERT: B 324 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6869 (pmm) REVERT: B 437 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7885 (tmt) REVERT: B 479 ILE cc_start: 0.5582 (OUTLIER) cc_final: 0.4971 (mm) REVERT: B 525 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8454 (p) REVERT: B 575 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7247 (pt0) outliers start: 29 outliers final: 7 residues processed: 125 average time/residue: 0.8886 time to fit residues: 119.8104 Evaluate side-chains 111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.0040 chunk 77 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 357 GLN B 512 HIS B 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106946 restraints weight = 8699.820| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.90 r_work: 0.2905 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7663 Z= 0.145 Angle : 0.497 6.866 10351 Z= 0.258 Chirality : 0.041 0.168 1177 Planarity : 0.003 0.034 1243 Dihedral : 13.977 104.782 1301 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.80 % Allowed : 21.73 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 940 helix: 2.03 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.74 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS A 620 PHE 0.014 0.001 PHE B 387 TYR 0.007 0.001 TYR B 371 ARG 0.005 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.750 Fit side-chains REVERT: A 285 GLU cc_start: 0.8302 (pm20) cc_final: 0.8075 (pm20) REVERT: A 324 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.5748 (ttt) REVERT: A 381 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8072 (t) REVERT: A 499 THR cc_start: 0.7677 (p) cc_final: 0.7433 (m) REVERT: A 568 LYS cc_start: 0.8017 (tttt) cc_final: 0.7239 (tttm) REVERT: B 211 LYS cc_start: 0.9082 (tttm) cc_final: 0.8811 (tttm) REVERT: B 280 ARG cc_start: 0.7308 (mpt90) cc_final: 0.6929 (mmt-90) REVERT: B 322 LEU cc_start: 0.7808 (mm) cc_final: 0.7525 (mm) REVERT: B 324 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6852 (pmm) REVERT: B 479 ILE cc_start: 0.5594 (OUTLIER) cc_final: 0.4970 (mm) REVERT: B 525 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 575 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7193 (pt0) outliers start: 21 outliers final: 9 residues processed: 119 average time/residue: 0.8950 time to fit residues: 114.8068 Evaluate side-chains 111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 GLN B 512 HIS B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.103734 restraints weight = 8877.821| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.91 r_work: 0.2852 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7663 Z= 0.199 Angle : 0.528 7.178 10351 Z= 0.275 Chirality : 0.042 0.167 1177 Planarity : 0.003 0.034 1243 Dihedral : 14.186 107.707 1300 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.20 % Allowed : 21.47 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 940 helix: 1.88 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.84 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 209 HIS 0.002 0.001 HIS A 512 PHE 0.017 0.001 PHE A 387 TYR 0.009 0.001 TYR B 673 ARG 0.006 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.839 Fit side-chains REVERT: A 285 GLU cc_start: 0.8286 (pm20) cc_final: 0.8068 (pm20) REVERT: A 315 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: A 324 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.5894 (ttt) REVERT: A 381 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8310 (t) REVERT: A 499 THR cc_start: 0.7627 (p) cc_final: 0.7354 (m) REVERT: A 568 LYS cc_start: 0.8103 (tttt) cc_final: 0.7305 (tttm) REVERT: A 634 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8333 (ttmt) REVERT: B 211 LYS cc_start: 0.9038 (tttm) cc_final: 0.8796 (tttm) REVERT: B 225 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.6113 (mpt) REVERT: B 280 ARG cc_start: 0.7243 (mpt90) cc_final: 0.6815 (mmt-90) REVERT: B 322 LEU cc_start: 0.7688 (mm) cc_final: 0.7427 (mm) REVERT: B 324 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6895 (pmm) REVERT: B 525 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8421 (p) REVERT: B 575 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7092 (pt0) outliers start: 24 outliers final: 8 residues processed: 115 average time/residue: 0.9392 time to fit residues: 116.3684 Evaluate side-chains 107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106072 restraints weight = 8870.983| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.92 r_work: 0.2877 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.8007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7663 Z= 0.158 Angle : 0.504 9.294 10351 Z= 0.261 Chirality : 0.042 0.172 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.818 104.447 1300 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.67 % Allowed : 22.00 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.29), residues: 940 helix: 2.10 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.015 0.001 PHE B 387 TYR 0.007 0.001 TYR B 371 ARG 0.004 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.779 Fit side-chains REVERT: A 285 GLU cc_start: 0.8305 (pm20) cc_final: 0.8071 (pm20) REVERT: A 324 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.5986 (ttt) REVERT: A 381 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8144 (t) REVERT: A 499 THR cc_start: 0.7640 (p) cc_final: 0.7359 (m) REVERT: A 572 LYS cc_start: 0.5895 (pmtt) cc_final: 0.5147 (mmtm) REVERT: A 634 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8344 (ttmt) REVERT: B 211 LYS cc_start: 0.9050 (tttm) cc_final: 0.8817 (tttm) REVERT: B 280 ARG cc_start: 0.7274 (mpt90) cc_final: 0.6860 (mmt-90) REVERT: B 322 LEU cc_start: 0.7719 (mm) cc_final: 0.7478 (mm) REVERT: B 324 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6883 (pmm) REVERT: B 525 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8422 (p) outliers start: 20 outliers final: 7 residues processed: 112 average time/residue: 0.9525 time to fit residues: 115.0916 Evaluate side-chains 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095383 restraints weight = 9053.965| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.02 r_work: 0.2877 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.8122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7663 Z= 0.150 Angle : 0.507 9.354 10351 Z= 0.261 Chirality : 0.041 0.169 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.631 102.917 1300 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.27 % Allowed : 22.40 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.29), residues: 940 helix: 2.09 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.015 0.001 PHE B 387 TYR 0.006 0.001 TYR B 371 ARG 0.004 0.000 ARG A 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.752 Fit side-chains REVERT: A 285 GLU cc_start: 0.8371 (pm20) cc_final: 0.8139 (pm20) REVERT: A 324 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.5829 (ttt) REVERT: A 381 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8124 (t) REVERT: A 391 ASP cc_start: 0.7824 (t0) cc_final: 0.7474 (m-30) REVERT: A 470 THR cc_start: 0.8554 (p) cc_final: 0.8333 (t) REVERT: A 572 LYS cc_start: 0.5940 (pmtt) cc_final: 0.5281 (mmtm) REVERT: A 634 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8390 (ttmt) REVERT: B 211 LYS cc_start: 0.9056 (tttm) cc_final: 0.8842 (tttm) REVERT: B 280 ARG cc_start: 0.7343 (mpt90) cc_final: 0.6949 (mmt-90) REVERT: B 322 LEU cc_start: 0.7787 (mm) cc_final: 0.7544 (mm) REVERT: B 324 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6853 (pmm) REVERT: B 525 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8442 (p) REVERT: B 573 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6414 (p0) REVERT: B 575 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7231 (pt0) outliers start: 17 outliers final: 6 residues processed: 112 average time/residue: 0.8648 time to fit residues: 104.7357 Evaluate side-chains 107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096042 restraints weight = 8986.502| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.97 r_work: 0.2865 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.8174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7663 Z= 0.174 Angle : 0.527 11.900 10351 Z= 0.269 Chirality : 0.042 0.170 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.729 103.712 1300 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.13 % Allowed : 22.80 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 940 helix: 2.04 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.015 0.001 PHE B 387 TYR 0.007 0.001 TYR B 570 ARG 0.005 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4737.46 seconds wall clock time: 84 minutes 44.59 seconds (5084.59 seconds total)