Starting phenix.real_space_refine on Fri Aug 22 20:30:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nph_0470/08_2025/6nph_0470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nph_0470/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6nph_0470/08_2025/6nph_0470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nph_0470/08_2025/6nph_0470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nph_0470/08_2025/6nph_0470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nph_0470/08_2025/6nph_0470.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.16, per 1000 atoms: 0.29 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: 0.63 Conformation dependent library (CDL) restraints added in 527.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.22 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: 1.10 Time building geometry restraints manager: 0.83 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 703 or resid 706)) selection = (chain 'B' and (resid 206 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: 0.800 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 18.600 ------------------------------------------------------------------------------- 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 7665 Z= 0.568 Angle : 1.415 31.111 10355 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG B 280 TYR 0.010 0.002 TYR B 491 PHE 0.032 0.003 PHE B 387 TRP 0.012 0.002 TRP A 657 HIS 0.003 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.01220 ( 7663) covalent geometry : angle 1.41548 (10351) SS BOND : bond 0.00493 ( 2) SS BOND : angle 0.74530 ( 4) hydrogen bonds : bond 0.17575 ( 428) hydrogen bonds : angle 6.57054 ( 1272) *********************** 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 : 0.276 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: 0.4082 time to fit residues: 93.3800 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 : 0.260 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 513 ASN B 664 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111613 restraints weight = 8476.953| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.83 r_work: 0.2977 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7665 Z= 0.147 Angle : 0.609 9.794 10355 Z= 0.316 Chirality : 0.043 0.192 1177 Planarity : 0.004 0.055 1243 Dihedral : 16.997 113.143 1309 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.20 % Allowed : 16.13 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.25), residues: 940 helix: -0.26 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -3.33 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 630 TYR 0.013 0.001 TYR A 371 PHE 0.016 0.001 PHE B 415 TRP 0.021 0.002 TRP B 209 HIS 0.003 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7663) covalent geometry : angle 0.60901 (10351) SS BOND : bond 0.01033 ( 2) SS BOND : angle 0.99068 ( 4) hydrogen bonds : bond 0.04119 ( 428) hydrogen bonds : angle 3.99691 ( 1272) *********************** 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 171 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.270 Fit side-chains REVERT: A 353 GLU cc_start: 0.6716 (tt0) cc_final: 0.6428 (tm-30) REVERT: A 525 SER cc_start: 0.7952 (p) cc_final: 0.7623 (p) REVERT: A 568 LYS cc_start: 0.7443 (tttt) cc_final: 0.6558 (tttm) REVERT: A 634 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8040 (ttmt) REVERT: B 304 MET cc_start: 0.8796 (ttp) cc_final: 0.8471 (ttp) REVERT: B 328 THR cc_start: 0.7918 (t) cc_final: 0.7595 (m) REVERT: B 345 ILE cc_start: 0.8368 (mt) cc_final: 0.8106 (mp) REVERT: B 479 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5037 (mm) REVERT: B 489 TYR cc_start: 0.6611 (m-80) cc_final: 0.6013 (m-80) REVERT: B 524 PHE cc_start: 0.7837 (t80) cc_final: 0.6930 (t80) REVERT: B 575 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7379 (pt0) outliers start: 39 outliers final: 11 residues processed: 154 average time/residue: 0.4205 time to fit residues: 69.7451 Evaluate side-chains 123 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 504 VAL Chi-restraints excluded: chain A residue 507 CYS 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 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 50 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 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 = 0.3591 r_free = 0.3591 target = 0.135675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105557 restraints weight = 8614.520| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.91 r_work: 0.2897 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7665 Z= 0.134 Angle : 0.559 7.817 10355 Z= 0.292 Chirality : 0.042 0.168 1177 Planarity : 0.004 0.042 1243 Dihedral : 16.418 111.347 1301 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.73 % Allowed : 19.33 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.27), residues: 940 helix: 0.76 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -3.15 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 404 TYR 0.012 0.001 TYR B 676 PHE 0.019 0.001 PHE A 387 TRP 0.019 0.002 TRP B 209 HIS 0.002 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7663) covalent geometry : angle 0.55880 (10351) SS BOND : bond 0.01772 ( 2) SS BOND : angle 0.66462 ( 4) hydrogen bonds : bond 0.04302 ( 428) hydrogen bonds : angle 3.74797 ( 1272) *********************** 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 148 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.253 Fit side-chains REVERT: A 211 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8615 (mtmt) REVERT: A 285 GLU cc_start: 0.8138 (pm20) cc_final: 0.7916 (pm20) REVERT: A 381 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8280 (t) REVERT: A 568 LYS cc_start: 0.7891 (tttt) cc_final: 0.7173 (tttm) REVERT: B 280 ARG cc_start: 0.7461 (mpt90) cc_final: 0.7252 (mmt-90) REVERT: B 315 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6282 (mt-10) REVERT: B 345 ILE cc_start: 0.8262 (mt) cc_final: 0.8058 (mp) REVERT: B 373 ILE cc_start: 0.8561 (pt) cc_final: 0.8198 (mt) REVERT: B 377 ILE cc_start: 0.9141 (mt) cc_final: 0.8854 (mp) REVERT: B 494 SER cc_start: 0.7196 (t) cc_final: 0.6860 (m) REVERT: B 525 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 575 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7251 (pt0) outliers start: 28 outliers final: 7 residues processed: 138 average time/residue: 0.3936 time to fit residues: 58.6059 Evaluate side-chains 106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS 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 507 CYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 363 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098098 restraints weight = 8930.913| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.91 r_work: 0.2974 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7665 Z= 0.224 Angle : 0.635 6.596 10355 Z= 0.331 Chirality : 0.046 0.169 1177 Planarity : 0.004 0.046 1243 Dihedral : 17.053 120.315 1301 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.93 % Allowed : 19.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.27), residues: 940 helix: 0.81 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -3.02 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 229 TYR 0.017 0.002 TYR B 673 PHE 0.023 0.002 PHE A 387 TRP 0.019 0.002 TRP B 209 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 7663) covalent geometry : angle 0.63521 (10351) SS BOND : bond 0.01248 ( 2) SS BOND : angle 1.03033 ( 4) hydrogen bonds : bond 0.05047 ( 428) hydrogen bonds : angle 3.96947 ( 1272) *********************** 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 130 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.287 Fit side-chains REVERT: A 225 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.6098 (mpt) REVERT: A 285 GLU cc_start: 0.8415 (pm20) cc_final: 0.8186 (pm20) REVERT: A 315 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: A 324 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.5908 (ttt) REVERT: A 381 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8519 (t) REVERT: A 549 LYS cc_start: 0.8069 (tptm) cc_final: 0.7435 (mmtp) REVERT: A 568 LYS cc_start: 0.8142 (tttt) cc_final: 0.7510 (tttm) REVERT: A 634 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8431 (ttmt) REVERT: B 211 LYS cc_start: 0.9122 (tttm) cc_final: 0.8900 (tttm) REVERT: B 345 ILE cc_start: 0.8409 (mt) cc_final: 0.8108 (mm) REVERT: B 407 THR cc_start: 0.8600 (p) cc_final: 0.8298 (p) REVERT: B 494 SER cc_start: 0.7353 (t) cc_final: 0.7109 (m) REVERT: B 525 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8159 (t) REVERT: B 575 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7317 (pt0) REVERT: B 677 LYS cc_start: 0.6515 (pttt) cc_final: 0.6229 (tttt) outliers start: 37 outliers final: 9 residues processed: 119 average time/residue: 0.4814 time to fit residues: 61.2849 Evaluate side-chains 94 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 363 ILE Chi-restraints excluded: chain A residue 375 SER 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 593 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 LEU 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 74 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 17 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.096710 restraints weight = 8964.423| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.01 r_work: 0.2867 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7665 Z= 0.105 Angle : 0.509 6.862 10355 Z= 0.267 Chirality : 0.041 0.161 1177 Planarity : 0.003 0.034 1243 Dihedral : 15.811 115.737 1301 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.00 % Allowed : 20.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.28), residues: 940 helix: 1.42 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.83 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.011 0.001 TYR B 676 PHE 0.012 0.001 PHE B 415 TRP 0.013 0.001 TRP B 209 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7663) covalent geometry : angle 0.50897 (10351) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.65156 ( 4) hydrogen bonds : bond 0.03736 ( 428) hydrogen bonds : angle 3.58022 ( 1272) *********************** 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 128 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.325 Fit side-chains REVERT: A 285 GLU cc_start: 0.8414 (pm20) cc_final: 0.8206 (pm20) REVERT: A 315 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: A 324 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6007 (ttt) REVERT: A 361 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8023 (tm) REVERT: A 381 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8343 (t) REVERT: A 568 LYS cc_start: 0.8070 (tttt) cc_final: 0.7306 (tttm) REVERT: A 634 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8455 (ttmt) REVERT: B 211 LYS cc_start: 0.9082 (tttm) cc_final: 0.8851 (tttm) REVERT: B 322 LEU cc_start: 0.7795 (mm) cc_final: 0.7534 (mm) REVERT: B 345 ILE cc_start: 0.8201 (mt) cc_final: 0.7972 (mm) REVERT: B 525 SER cc_start: 0.8547 (p) cc_final: 0.8263 (t) REVERT: B 575 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7262 (pt0) REVERT: B 583 THR cc_start: 0.8547 (t) cc_final: 0.8291 (m) outliers start: 30 outliers final: 5 residues processed: 119 average time/residue: 0.4092 time to fit residues: 52.4004 Evaluate side-chains 98 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 507 CYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 507 CYS 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 59 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092853 restraints weight = 8950.216| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.01 r_work: 0.2832 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7665 Z= 0.121 Angle : 0.517 5.778 10355 Z= 0.271 Chirality : 0.042 0.158 1177 Planarity : 0.003 0.033 1243 Dihedral : 15.477 109.622 1301 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.93 % Allowed : 22.53 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.28), residues: 940 helix: 1.58 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.80 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 497 TYR 0.012 0.001 TYR B 676 PHE 0.016 0.001 PHE A 387 TRP 0.013 0.001 TRP B 209 HIS 0.002 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7663) covalent geometry : angle 0.51667 (10351) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.23908 ( 4) hydrogen bonds : bond 0.03960 ( 428) hydrogen bonds : angle 3.55630 ( 1272) *********************** 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 117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.238 Fit side-chains REVERT: A 285 GLU cc_start: 0.8413 (pm20) cc_final: 0.8212 (pm20) REVERT: A 315 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: A 324 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.5949 (ttt) REVERT: A 361 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7959 (tm) REVERT: A 381 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (t) REVERT: A 568 LYS cc_start: 0.8069 (tttt) cc_final: 0.7308 (tttm) REVERT: A 634 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8433 (ttmt) REVERT: B 211 LYS cc_start: 0.9076 (tttm) cc_final: 0.8849 (tttm) REVERT: B 322 LEU cc_start: 0.7809 (mm) cc_final: 0.7569 (mm) REVERT: B 525 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8237 (t) outliers start: 22 outliers final: 5 residues processed: 108 average time/residue: 0.4614 time to fit residues: 53.1628 Evaluate side-chains 99 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 634 LYS 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 80 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.093665 restraints weight = 9080.057| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.03 r_work: 0.2869 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7665 Z= 0.164 Angle : 0.561 7.989 10355 Z= 0.293 Chirality : 0.043 0.166 1177 Planarity : 0.003 0.032 1243 Dihedral : 15.683 113.115 1300 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.47 % Allowed : 22.00 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.28), residues: 940 helix: 1.48 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.86 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 404 TYR 0.013 0.001 TYR B 676 PHE 0.019 0.002 PHE A 387 TRP 0.012 0.002 TRP B 209 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7663) covalent geometry : angle 0.56050 (10351) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.49235 ( 4) hydrogen bonds : bond 0.04417 ( 428) hydrogen bonds : angle 3.69113 ( 1272) *********************** 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 114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.278 Fit side-chains REVERT: A 225 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.6104 (mpt) REVERT: A 285 GLU cc_start: 0.8415 (pm20) cc_final: 0.8215 (pm20) REVERT: A 361 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8175 (tm) REVERT: A 381 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8400 (t) REVERT: A 497 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7263 (ptt-90) REVERT: A 568 LYS cc_start: 0.8101 (tttt) cc_final: 0.7358 (tttm) REVERT: A 634 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8472 (ttmt) REVERT: B 211 LYS cc_start: 0.9052 (tttm) cc_final: 0.8840 (tttm) REVERT: B 280 ARG cc_start: 0.8191 (mpt180) cc_final: 0.7991 (mmt180) REVERT: B 322 LEU cc_start: 0.7761 (mm) cc_final: 0.7538 (mm) REVERT: B 324 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7115 (pmm) REVERT: B 384 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.5251 (pptt) REVERT: B 525 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8205 (t) outliers start: 26 outliers final: 9 residues processed: 103 average time/residue: 0.4611 time to fit residues: 50.7450 Evaluate side-chains 101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 225 MET 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 345 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 384 LYS 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 541 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 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 512 HIS B 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.095500 restraints weight = 9003.639| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.97 r_work: 0.2854 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.8076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7665 Z= 0.101 Angle : 0.508 11.534 10355 Z= 0.264 Chirality : 0.041 0.161 1177 Planarity : 0.003 0.032 1243 Dihedral : 14.970 106.387 1300 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.40 % Allowed : 22.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.29), residues: 940 helix: 1.85 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.78 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.010 0.001 TYR B 676 PHE 0.012 0.001 PHE B 415 TRP 0.011 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7663) covalent geometry : angle 0.50726 (10351) SS BOND : bond 0.00121 ( 2) SS BOND : angle 1.24418 ( 4) hydrogen bonds : bond 0.03626 ( 428) hydrogen bonds : angle 3.47723 ( 1272) *********************** 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 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.305 Fit side-chains REVERT: A 285 GLU cc_start: 0.8374 (pm20) cc_final: 0.8159 (pm20) REVERT: A 315 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: A 361 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7968 (tm) REVERT: A 568 LYS cc_start: 0.8100 (tttt) cc_final: 0.7378 (tttm) REVERT: A 634 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8423 (ttmt) REVERT: B 211 LYS cc_start: 0.9061 (tttm) cc_final: 0.8823 (tttm) REVERT: B 280 ARG cc_start: 0.8138 (mpt180) cc_final: 0.7938 (mmt180) REVERT: B 322 LEU cc_start: 0.7804 (mm) cc_final: 0.7592 (mm) REVERT: B 324 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6967 (pmm) REVERT: B 525 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8330 (t) outliers start: 18 outliers final: 5 residues processed: 106 average time/residue: 0.4168 time to fit residues: 47.6796 Evaluate side-chains 101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 634 LYS Chi-restraints excluded: chain B residue 324 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 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.094125 restraints weight = 8979.558| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.01 r_work: 0.2847 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7665 Z= 0.111 Angle : 0.518 11.227 10355 Z= 0.268 Chirality : 0.041 0.159 1177 Planarity : 0.003 0.031 1243 Dihedral : 14.773 105.884 1300 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.13 % Allowed : 23.33 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.29), residues: 940 helix: 1.90 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.82 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.007 0.001 TYR B 371 PHE 0.015 0.001 PHE A 387 TRP 0.011 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7663) covalent geometry : angle 0.51704 (10351) SS BOND : bond 0.00108 ( 2) SS BOND : angle 1.44294 ( 4) hydrogen bonds : bond 0.03757 ( 428) hydrogen bonds : angle 3.48345 ( 1272) *********************** 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 109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.288 Fit side-chains REVERT: A 315 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: A 361 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7993 (tm) REVERT: A 497 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7190 (ptt-90) REVERT: A 518 MET cc_start: 0.8748 (mmt) cc_final: 0.8545 (mmt) REVERT: A 634 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8453 (ttmt) REVERT: B 211 LYS cc_start: 0.9067 (tttm) cc_final: 0.8837 (tttm) REVERT: B 322 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7592 (mm) REVERT: B 324 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6956 (pmm) REVERT: B 525 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8320 (t) REVERT: B 575 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7152 (pt0) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 0.4571 time to fit residues: 49.1651 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 : 0.270 ------------------------------------------------------------------------------- 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 497 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.124566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.093166 restraints weight = 8902.258| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.03 r_work: 0.2840 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7665 Z= 0.125 Angle : 0.529 11.041 10355 Z= 0.274 Chirality : 0.042 0.160 1177 Planarity : 0.003 0.031 1243 Dihedral : 14.828 106.981 1300 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.87 % Allowed : 24.13 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.29), residues: 940 helix: 1.87 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.77 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.008 0.001 TYR A 676 PHE 0.016 0.001 PHE A 387 TRP 0.011 0.001 TRP B 209 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7663) covalent geometry : angle 0.52842 (10351) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.30071 ( 4) hydrogen bonds : bond 0.03939 ( 428) hydrogen bonds : angle 3.52782 ( 1272) ********************** 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 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.284 Fit side-chains REVERT: A 225 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.6313 (mpt) REVERT: A 315 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: A 361 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7991 (tm) REVERT: A 407 THR cc_start: 0.8309 (p) cc_final: 0.8104 (p) REVERT: A 497 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7147 (ptt-90) REVERT: A 572 LYS cc_start: 0.6065 (pmtt) cc_final: 0.5345 (mmtm) REVERT: A 634 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8443 (ttmt) REVERT: B 211 LYS cc_start: 0.9059 (tttm) cc_final: 0.8837 (tttm) REVERT: B 322 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7536 (mm) REVERT: B 324 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7072 (pmm) REVERT: B 525 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8311 (t) REVERT: B 575 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7118 (pt0) outliers start: 14 outliers final: 5 residues processed: 93 average time/residue: 0.4676 time to fit residues: 46.9025 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL 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 361 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.0020 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097433 restraints weight = 8809.363| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.03 r_work: 0.2911 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.8244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7665 Z= 0.095 Angle : 0.496 10.833 10355 Z= 0.257 Chirality : 0.040 0.157 1177 Planarity : 0.003 0.031 1243 Dihedral : 14.327 101.420 1300 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.87 % Allowed : 24.00 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.29), residues: 940 helix: 2.12 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.67 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 332 TYR 0.006 0.001 TYR B 371 PHE 0.010 0.001 PHE A 359 TRP 0.011 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 7663) covalent geometry : angle 0.49541 (10351) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.18900 ( 4) hydrogen bonds : bond 0.03389 ( 428) hydrogen bonds : angle 3.35559 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2361.89 seconds wall clock time: 41 minutes 6.71 seconds (2466.71 seconds total)