Starting phenix.real_space_refine on Wed Mar 12 10:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nph_0470/03_2025/6nph_0470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nph_0470/03_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_0470/03_2025/6nph_0470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nph_0470/03_2025/6nph_0470.map" model { file = "/net/cci-nas-00/data/ceres_data/6nph_0470/03_2025/6nph_0470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nph_0470/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.09, per 1000 atoms: 0.81 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.68 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: 1.98 Time building geometry restraints manager: 2.29 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: 37.030 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.160 Find NCS groups from input model: 0.320 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:21.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.250 ------------------------------------------------------------------------------- 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 : 0.737 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: 0.8500 time to fit residues: 194.8768 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 : 0.687 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113520 restraints weight = 8452.930| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.84 r_work: 0.3191 rms_B_bonded: 2.65 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 12.977 10351 Z= 0.315 Chirality : 0.043 0.161 1177 Planarity : 0.004 0.054 1243 Dihedral : 16.533 105.556 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 : 0.611 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: 0.8697 (ttp) REVERT: B 345 ILE cc_start: 0.8532 (mt) cc_final: 0.8262 (mp) REVERT: B 364 LEU cc_start: 0.7676 (tp) cc_final: 0.7416 (tt) REVERT: B 373 ILE cc_start: 0.8438 (pt) cc_final: 0.7941 (mt) REVERT: B 479 ILE cc_start: 0.5618 (OUTLIER) cc_final: 0.5092 (mm) REVERT: B 524 PHE cc_start: 0.8019 (t80) cc_final: 0.7183 (t80) REVERT: B 549 LYS cc_start: 0.8149 (tptm) cc_final: 0.7732 (tppt) REVERT: B 575 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7494 (pt0) outliers start: 41 outliers final: 11 residues processed: 157 average time/residue: 1.1071 time to fit residues: 188.5809 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 : 0.860 ------------------------------------------------------------------------------- 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: 0.5980 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.138578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108579 restraints weight = 8580.541| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.92 r_work: 0.3124 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5817 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= 0.151 Angle : 0.526 8.293 10351 Z= 0.274 Chirality : 0.041 0.167 1177 Planarity : 0.003 0.042 1243 Dihedral : 15.870 107.829 1301 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.20 % Allowed : 19.60 % Favored : 77.20 % 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: -0.48 (0.27), residues: 940 helix: 1.03 (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 0.016 0.001 TRP B 209 HIS 0.002 0.001 HIS B 620 PHE 0.015 0.001 PHE A 387 TYR 0.009 0.001 TYR B 570 ARG 0.002 0.000 ARG B 332 *********************** 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 150 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.851 Fit side-chains REVERT: A 285 GLU cc_start: 0.8078 (pm20) cc_final: 0.7824 (pm20) REVERT: A 340 ILE cc_start: 0.8393 (pp) cc_final: 0.8176 (pt) REVERT: A 381 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 568 LYS cc_start: 0.7692 (tttt) cc_final: 0.7057 (tttm) REVERT: A 570 TYR cc_start: 0.7960 (m-80) cc_final: 0.7585 (m-80) REVERT: B 304 MET cc_start: 0.9078 (ttp) cc_final: 0.8827 (ttp) REVERT: B 315 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6179 (mt-10) REVERT: B 345 ILE cc_start: 0.8318 (mt) cc_final: 0.7997 (mm) REVERT: B 373 ILE cc_start: 0.8528 (pt) cc_final: 0.8078 (mt) REVERT: B 377 ILE cc_start: 0.9133 (mt) cc_final: 0.8849 (mp) REVERT: B 494 SER cc_start: 0.7331 (t) cc_final: 0.6931 (m) REVERT: B 575 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7483 (pt0) outliers start: 24 outliers final: 8 residues processed: 142 average time/residue: 1.0811 time to fit residues: 167.6323 Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 362 VAL 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 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: 0.6980 chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 73 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108003 restraints weight = 8600.249| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.88 r_work: 0.2960 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6821 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= 0.155 Angle : 0.508 6.870 10351 Z= 0.265 Chirality : 0.041 0.165 1177 Planarity : 0.003 0.037 1243 Dihedral : 14.997 107.089 1301 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.47 % Allowed : 21.60 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 940 helix: 1.47 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.94 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.014 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 138 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.883 Fit side-chains REVERT: A 285 GLU cc_start: 0.8170 (pm20) cc_final: 0.7910 (pm20) REVERT: A 324 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.5521 (ttt) REVERT: A 568 LYS cc_start: 0.7956 (tttt) cc_final: 0.7216 (tttm) REVERT: A 570 TYR cc_start: 0.8151 (m-80) cc_final: 0.7701 (m-80) REVERT: A 577 LEU cc_start: 0.7098 (mt) cc_final: 0.6654 (mp) REVERT: B 280 ARG cc_start: 0.7489 (mpt90) cc_final: 0.7266 (mmt-90) REVERT: B 315 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6312 (mt-10) REVERT: B 377 ILE cc_start: 0.9151 (mt) cc_final: 0.8896 (mp) REVERT: B 479 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.4957 (mm) REVERT: B 525 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7919 (t) REVERT: B 575 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7253 (pt0) REVERT: B 583 THR cc_start: 0.8713 (t) cc_final: 0.8420 (m) outliers start: 26 outliers final: 10 residues processed: 128 average time/residue: 0.7668 time to fit residues: 107.6148 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 : 0.744 ------------------------------------------------------------------------------- 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 516 GLN Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 315 GLU 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: 7.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 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: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103158 restraints weight = 8633.136| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.92 r_work: 0.2894 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.7432 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= 0.191 Angle : 0.519 7.862 10351 Z= 0.270 Chirality : 0.042 0.161 1177 Planarity : 0.003 0.037 1243 Dihedral : 14.819 109.785 1301 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.60 % Allowed : 21.60 % Favored : 74.80 % 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: 0.18 (0.28), residues: 940 helix: 1.51 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.93 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 209 HIS 0.003 0.001 HIS B 512 PHE 0.016 0.001 PHE A 387 TYR 0.010 0.001 TYR B 673 ARG 0.002 0.000 ARG A 229 *********************** 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 132 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.735 Fit side-chains REVERT: A 285 GLU cc_start: 0.8275 (pm20) cc_final: 0.7970 (pm20) REVERT: A 324 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.5762 (ttt) REVERT: A 381 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8343 (t) REVERT: A 568 LYS cc_start: 0.8088 (tttt) cc_final: 0.7424 (tttm) REVERT: A 634 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8373 (ttmt) REVERT: B 211 LYS cc_start: 0.9117 (tttm) cc_final: 0.8856 (tttm) REVERT: B 280 ARG cc_start: 0.7444 (mpt90) cc_final: 0.7096 (mmt-90) REVERT: B 315 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6557 (mt-10) REVERT: B 322 LEU cc_start: 0.7950 (mm) cc_final: 0.7676 (mm) REVERT: B 324 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6943 (pmm) REVERT: B 437 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7931 (tmt) REVERT: B 479 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5158 (mm) REVERT: B 494 SER cc_start: 0.7165 (t) cc_final: 0.6906 (m) REVERT: B 525 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 575 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7243 (pt0) REVERT: B 583 THR cc_start: 0.8712 (t) cc_final: 0.8437 (m) outliers start: 27 outliers final: 7 residues processed: 126 average time/residue: 0.8646 time to fit residues: 117.8241 Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 MET 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 A residue 610 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097051 restraints weight = 8736.000| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.96 r_work: 0.2885 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7663 Z= 0.152 Angle : 0.496 6.615 10351 Z= 0.259 Chirality : 0.041 0.175 1177 Planarity : 0.003 0.036 1243 Dihedral : 14.392 106.310 1301 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.33 % Allowed : 21.07 % Favored : 75.60 % 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: 0.62 (0.28), residues: 940 helix: 1.92 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 322 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 0.013 0.001 PHE B 415 TYR 0.009 0.001 TYR B 676 ARG 0.003 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 127 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.714 Fit side-chains REVERT: A 285 GLU cc_start: 0.8363 (pm20) cc_final: 0.8121 (pm20) REVERT: A 315 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: A 324 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.5813 (ttt) REVERT: A 361 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8026 (tm) REVERT: A 381 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8338 (t) REVERT: A 634 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8365 (ttmt) REVERT: B 211 LYS cc_start: 0.9119 (tttm) cc_final: 0.8871 (tttm) REVERT: B 280 ARG cc_start: 0.7393 (mpt90) cc_final: 0.7036 (mmt-90) REVERT: B 322 LEU cc_start: 0.7862 (mm) cc_final: 0.7585 (mm) REVERT: B 479 ILE cc_start: 0.5734 (OUTLIER) cc_final: 0.5127 (mm) REVERT: B 494 SER cc_start: 0.7033 (t) cc_final: 0.6812 (m) REVERT: B 525 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 575 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7229 (pt0) outliers start: 25 outliers final: 10 residues processed: 120 average time/residue: 0.8542 time to fit residues: 110.7858 Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 361 LEU 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 316 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 395 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 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: 0.9980 chunk 75 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 35 optimal weight: 0.0060 chunk 73 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107659 restraints weight = 8746.861| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.88 r_work: 0.2909 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.7820 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= 0.142 Angle : 0.490 6.847 10351 Z= 0.256 Chirality : 0.041 0.170 1177 Planarity : 0.003 0.034 1243 Dihedral : 13.969 104.526 1300 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.80 % Allowed : 21.33 % Favored : 75.87 % 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: 0.81 (0.28), residues: 940 helix: 2.05 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.76 (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 0.013 0.001 PHE B 387 TYR 0.008 0.001 TYR B 676 ARG 0.002 0.000 ARG B 404 *********************** 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 128 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.786 Fit side-chains REVERT: A 285 GLU cc_start: 0.8355 (pm20) cc_final: 0.8105 (pm20) REVERT: A 315 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: A 324 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.5785 (ttt) REVERT: A 350 MET cc_start: 0.7723 (mmm) cc_final: 0.7068 (tpp) REVERT: A 499 THR cc_start: 0.7635 (p) cc_final: 0.7388 (m) REVERT: A 568 LYS cc_start: 0.8064 (tttt) cc_final: 0.7303 (tttm) REVERT: A 634 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8368 (ttmt) REVERT: B 211 LYS cc_start: 0.9086 (tttm) cc_final: 0.8832 (tttm) REVERT: B 280 ARG cc_start: 0.7350 (mpt90) cc_final: 0.6973 (mmt-90) REVERT: B 322 LEU cc_start: 0.7851 (mm) cc_final: 0.7578 (mm) REVERT: B 479 ILE cc_start: 0.5624 (OUTLIER) cc_final: 0.4996 (mm) REVERT: B 525 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8494 (p) REVERT: B 575 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7170 (pt0) REVERT: B 583 THR cc_start: 0.8594 (t) cc_final: 0.8346 (m) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.8807 time to fit residues: 113.0521 Evaluate side-chains 114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET 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 316 LEU 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: 0.9980 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.093899 restraints weight = 9094.515| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.97 r_work: 0.2871 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7663 Z= 0.176 Angle : 0.509 6.425 10351 Z= 0.266 Chirality : 0.042 0.168 1177 Planarity : 0.003 0.033 1243 Dihedral : 14.021 105.872 1300 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.80 % Allowed : 21.33 % Favored : 75.87 % 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: 0.82 (0.28), residues: 940 helix: 2.03 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.73 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 209 HIS 0.002 0.001 HIS A 512 PHE 0.015 0.001 PHE B 387 TYR 0.007 0.001 TYR B 673 ARG 0.002 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 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.042 Fit side-chains REVERT: A 285 GLU cc_start: 0.8410 (pm20) cc_final: 0.8192 (pm20) REVERT: A 315 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: A 324 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.5907 (ttt) REVERT: A 350 MET cc_start: 0.7917 (mmm) cc_final: 0.7324 (tpp) REVERT: A 361 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7989 (tm) REVERT: A 381 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8392 (t) REVERT: A 499 THR cc_start: 0.7697 (p) cc_final: 0.7428 (m) REVERT: A 634 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8409 (ttmt) REVERT: B 211 LYS cc_start: 0.9069 (tttm) cc_final: 0.8839 (tttm) REVERT: B 280 ARG cc_start: 0.7411 (mpt90) cc_final: 0.7025 (mmt-90) REVERT: B 322 LEU cc_start: 0.7793 (mm) cc_final: 0.7528 (mm) REVERT: B 324 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6940 (pmm) REVERT: B 525 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8515 (p) REVERT: B 575 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7164 (pt0) outliers start: 21 outliers final: 8 residues processed: 109 average time/residue: 0.9718 time to fit residues: 113.9874 Evaluate side-chains 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 361 LEU 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 324 MET Chi-restraints excluded: chain B residue 364 LEU 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: 7.9990 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 75 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094442 restraints weight = 9105.278| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.98 r_work: 0.2869 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.8062 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= 0.162 Angle : 0.497 6.128 10351 Z= 0.260 Chirality : 0.042 0.175 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.841 104.081 1300 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.53 % Allowed : 21.60 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 940 helix: 2.12 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.65 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 209 HIS 0.003 0.001 HIS B 620 PHE 0.014 0.001 PHE B 387 TYR 0.006 0.001 TYR B 676 ARG 0.002 0.000 ARG B 404 *********************** 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 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.767 Fit side-chains REVERT: A 285 GLU cc_start: 0.8378 (pm20) cc_final: 0.8143 (pm20) REVERT: A 315 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: A 324 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6008 (ttt) REVERT: A 361 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8000 (tm) REVERT: A 381 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8223 (t) REVERT: A 437 MET cc_start: 0.7837 (tmt) cc_final: 0.7602 (tmt) REVERT: A 499 THR cc_start: 0.7647 (p) cc_final: 0.7352 (m) REVERT: A 634 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8381 (ttmt) REVERT: B 211 LYS cc_start: 0.9069 (tttm) cc_final: 0.8854 (tttm) REVERT: B 280 ARG cc_start: 0.7387 (mpt90) cc_final: 0.6985 (mmt-90) REVERT: B 322 LEU cc_start: 0.7781 (mm) cc_final: 0.7534 (mm) REVERT: B 324 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6874 (pmm) REVERT: B 525 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8467 (p) outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 0.9006 time to fit residues: 106.8183 Evaluate side-chains 110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 361 LEU 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 307 VAL 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 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: 5.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.093480 restraints weight = 9065.012| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.95 r_work: 0.2851 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7663 Z= 0.185 Angle : 0.512 6.035 10351 Z= 0.267 Chirality : 0.042 0.178 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.871 105.544 1300 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.53 % Allowed : 21.60 % Favored : 75.87 % 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: 0.91 (0.28), residues: 940 helix: 2.07 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.62 (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 A 387 TYR 0.007 0.001 TYR B 676 ARG 0.002 0.000 ARG B 404 ********************** 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 109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.777 Fit side-chains REVERT: A 285 GLU cc_start: 0.8341 (pm20) cc_final: 0.8122 (pm20) REVERT: A 361 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7910 (tm) REVERT: A 381 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8183 (t) REVERT: A 437 MET cc_start: 0.7800 (tmt) cc_final: 0.7568 (tmt) REVERT: A 572 LYS cc_start: 0.6078 (pmtt) cc_final: 0.5358 (mmtm) REVERT: A 634 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8390 (ttmt) REVERT: B 211 LYS cc_start: 0.9075 (tttm) cc_final: 0.8828 (tttm) REVERT: B 280 ARG cc_start: 0.7259 (mpt90) cc_final: 0.6896 (mmt-90) REVERT: B 322 LEU cc_start: 0.7701 (mm) cc_final: 0.7474 (mm) REVERT: B 324 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7003 (pmm) REVERT: B 525 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8426 (p) outliers start: 19 outliers final: 9 residues processed: 103 average time/residue: 0.9748 time to fit residues: 108.1139 Evaluate side-chains 103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 361 LEU 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 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: 0.8980 chunk 80 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.094231 restraints weight = 8990.285| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.93 r_work: 0.2858 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.8191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7663 Z= 0.175 Angle : 0.516 11.232 10351 Z= 0.266 Chirality : 0.042 0.166 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.803 104.391 1300 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.53 % Allowed : 21.87 % Favored : 75.60 % 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: 0.98 (0.28), residues: 940 helix: 2.11 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.56 (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 0.014 0.001 PHE B 387 TYR 0.006 0.001 TYR B 676 ARG 0.002 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5392.33 seconds wall clock time: 96 minutes 39.13 seconds (5799.13 seconds total)