Starting phenix.real_space_refine on Fri Sep 11 04:45:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nph_0470/09_2026/6nph_0470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nph_0470/09_2026/6nph_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_0470/09_2026/6nph_0470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nph_0470/09_2026/6nph_0470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nph_0470/09_2026/6nph_0470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nph_0470/09_2026/6nph_0470.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nph_0470/09_2026/6nph_0470.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nph_0470/09_2026/6nph_0470.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.90, per 1000 atoms: 0.25 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: 0.73 Conformation dependent library (CDL) restraints added in 614.4 milliseconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 70.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 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: 0.91 Time building geometry restraints manager: 0.98 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: 4208 28.94 - 57.87: 190 57.87 - 86.81: 27 86.81 - 115.75: 5 115.75 - 144.68: 5 Dihedral angle restraints: 4435 sinusoidal: 1749 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 4432 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.470 Find NCS groups from input model: 0.150 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:9.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 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 : 17.825 144.683 2721 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 are 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/Z covalent geometry : bond 0.01220 / 0.57 ( 7663) covalent geometry : angle 1.41548 / 0.63 (10351) SS BOND : bond 0.00493 / 0.25 ( 2) SS BOND : angle 0.74530 / 0.38 ( 4) hydrogen bonds : bond 0.17575 / 11.71 ( 428) hydrogen bonds : angle 6.57054 / 4.63 ( 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 : 0.179 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: 0.7555 (mt-10) cc_final: 0.7341 (pt0) outliers start: 35 outliers final: 6 residues processed: 213 average time/residue: 0.3633 time to fit residues: 83.2942 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 : 0.152 ------------------------------------------------------------------------------- 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... 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 = 0.3646 r_free = 0.3646 target = 0.140184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110322 restraints weight = 8510.931| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.84 r_work: 0.2983 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7665 Z= 0.135 Angle : 0.631 13.086 10355 Z= 0.317 Chirality : 0.043 0.195 1177 Planarity : 0.004 0.055 1243 Dihedral : 16.075 108.931 1267 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.20 % Allowed : 16.00 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.25), residues: 940 helix: -0.16 (0.20), residues: 620 sheet: None (None), residues: 0 loop : -3.24 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 630 TYR 0.013 0.001 TYR A 371 PHE 0.016 0.001 PHE A 415 TRP 0.021 0.002 TRP B 209 HIS 0.003 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7663) covalent geometry : angle 0.63091 / 0.32 (10351) SS BOND : bond 0.01081 / 0.57 ( 2) SS BOND : angle 1.08202 / 0.63 ( 4) hydrogen bonds : bond 0.04098 / 2.82 ( 428) hydrogen bonds : angle 3.99950 / 2.82 ( 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 169 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.210 Fit side-chains REVERT: A 353 GLU cc_start: 0.6716 (tt0) cc_final: 0.6411 (tm-30) REVERT: A 525 SER cc_start: 0.7940 (p) cc_final: 0.7625 (p) REVERT: A 568 LYS cc_start: 0.7469 (tttt) cc_final: 0.6545 (tttm) REVERT: A 634 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8031 (ttmt) REVERT: B 304 MET cc_start: 0.8817 (ttp) cc_final: 0.8505 (ttp) REVERT: B 328 THR cc_start: 0.7830 (t) cc_final: 0.7537 (m) REVERT: B 345 ILE cc_start: 0.8330 (mt) cc_final: 0.8059 (mp) REVERT: B 479 ILE cc_start: 0.5530 (OUTLIER) cc_final: 0.5007 (mm) REVERT: B 524 PHE cc_start: 0.7839 (t80) cc_final: 0.6756 (t80) REVERT: B 575 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7348 (pt0) outliers start: 39 outliers final: 11 residues processed: 152 average time/residue: 0.3552 time to fit residues: 58.4250 Evaluate side-chains 121 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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: 0.0980 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 0.0170 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 427 ASN B 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110140 restraints weight = 8511.371| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.86 r_work: 0.2982 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7665 Z= 0.116 Angle : 0.528 6.837 10355 Z= 0.276 Chirality : 0.040 0.162 1177 Planarity : 0.003 0.042 1243 Dihedral : 15.032 105.086 1259 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.47 % Allowed : 19.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 940 helix: 0.86 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -3.15 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.009 0.001 TYR B 570 PHE 0.013 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/Z covalent geometry : bond 0.00236 / 0.12 ( 7663) covalent geometry : angle 0.52736 / 0.28 (10351) SS BOND : bond 0.00460 / 0.22 ( 2) SS BOND : angle 0.86889 / 0.44 ( 4) hydrogen bonds : bond 0.03836 / 2.62 ( 428) hydrogen bonds : angle 3.57176 / 2.50 ( 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 151 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.234 Fit side-chains REVERT: A 211 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8384 (mtmt) REVERT: A 285 GLU cc_start: 0.7982 (pm20) cc_final: 0.7716 (pm20) REVERT: A 381 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8115 (t) REVERT: A 568 LYS cc_start: 0.7669 (tttt) cc_final: 0.6958 (tttm) REVERT: A 570 TYR cc_start: 0.7942 (m-80) cc_final: 0.7535 (m-80) REVERT: B 304 MET cc_start: 0.8951 (ttp) cc_final: 0.8560 (ttp) REVERT: B 315 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6045 (mt-10) REVERT: B 345 ILE cc_start: 0.8143 (mt) cc_final: 0.7846 (mm) REVERT: B 373 ILE cc_start: 0.8432 (pt) cc_final: 0.8079 (mt) REVERT: B 377 ILE cc_start: 0.9081 (mt) cc_final: 0.8788 (mp) REVERT: B 525 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7925 (t) REVERT: B 575 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7410 (pt0) outliers start: 26 outliers final: 7 residues processed: 143 average time/residue: 0.3284 time to fit residues: 51.1303 Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 315 GLU 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: 6.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100288 restraints weight = 8897.261| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.91 r_work: 0.2829 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7665 Z= 0.151 Angle : 0.569 6.976 10355 Z= 0.296 Chirality : 0.043 0.175 1177 Planarity : 0.004 0.045 1243 Dihedral : 15.329 108.015 1259 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.20 % Allowed : 21.73 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 940 helix: 1.12 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -3.09 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.012 0.001 TYR B 676 PHE 0.018 0.001 PHE B 415 TRP 0.018 0.002 TRP B 209 HIS 0.004 0.001 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 7663) covalent geometry : angle 0.56861 / 0.30 (10351) SS BOND : bond 0.00145 / 0.07 ( 2) SS BOND : angle 0.31097 / 0.14 ( 4) hydrogen bonds : bond 0.04394 / 3.03 ( 428) hydrogen bonds : angle 3.76980 / 2.63 ( 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 127 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 285 GLU cc_start: 0.8131 (pm20) cc_final: 0.7851 (pm20) REVERT: A 324 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.5719 (ttt) REVERT: A 522 SER cc_start: 0.8140 (t) cc_final: 0.7933 (p) REVERT: A 568 LYS cc_start: 0.8059 (tttt) cc_final: 0.7237 (tttm) REVERT: A 634 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8331 (ttmt) REVERT: B 211 LYS cc_start: 0.9048 (tttm) cc_final: 0.8770 (tttm) REVERT: B 315 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: B 345 ILE cc_start: 0.8167 (mt) cc_final: 0.7902 (mm) REVERT: B 479 ILE cc_start: 0.5867 (OUTLIER) cc_final: 0.5299 (mm) REVERT: B 494 SER cc_start: 0.7013 (t) cc_final: 0.6732 (m) REVERT: B 575 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7183 (pt0) REVERT: B 583 THR cc_start: 0.8558 (t) cc_final: 0.8313 (m) REVERT: B 677 LYS cc_start: 0.6259 (pttt) cc_final: 0.5939 (tttt) outliers start: 24 outliers final: 6 residues processed: 121 average time/residue: 0.3682 time to fit residues: 48.2351 Evaluate side-chains 99 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS 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: 6.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3529 r_free = 0.3529 target = 0.131937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.101705 restraints weight = 8791.813| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.94 r_work: 0.2874 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.7556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7665 Z= 0.106 Angle : 0.504 6.917 10355 Z= 0.263 Chirality : 0.041 0.163 1177 Planarity : 0.003 0.037 1243 Dihedral : 14.443 102.248 1259 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.20 % Allowed : 20.80 % Favored : 76.00 % 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 are not related in a simple way. whole: 0.27 (0.28), residues: 940 helix: 1.56 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.88 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 332 TYR 0.011 0.001 TYR B 676 PHE 0.013 0.001 PHE B 415 TRP 0.014 0.001 TRP B 209 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 7663) covalent geometry : angle 0.50413 / 0.26 (10351) SS BOND : bond 0.00492 / 0.26 ( 2) SS BOND : angle 0.62978 / 0.33 ( 4) hydrogen bonds : bond 0.03725 / 2.56 ( 428) hydrogen bonds : angle 3.51035 / 2.45 ( 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 130 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.199 Fit side-chains REVERT: A 285 GLU cc_start: 0.8206 (pm20) cc_final: 0.7947 (pm20) REVERT: A 315 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 324 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.5777 (ttt) REVERT: A 361 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7889 (tm) REVERT: A 381 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8261 (t) REVERT: A 492 ASP cc_start: 0.8250 (t70) cc_final: 0.8008 (t70) REVERT: A 568 LYS cc_start: 0.8043 (tttt) cc_final: 0.7319 (tttm) REVERT: B 211 LYS cc_start: 0.9070 (tttm) cc_final: 0.8810 (tttm) REVERT: B 322 LEU cc_start: 0.7728 (mm) cc_final: 0.7426 (mm) REVERT: B 324 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6898 (pmm) REVERT: B 345 ILE cc_start: 0.8157 (mt) cc_final: 0.7921 (mm) REVERT: B 479 ILE cc_start: 0.5786 (OUTLIER) cc_final: 0.5171 (mm) REVERT: B 494 SER cc_start: 0.7116 (t) cc_final: 0.6866 (m) REVERT: B 525 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8089 (t) REVERT: B 575 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7205 (pt0) REVERT: B 677 LYS cc_start: 0.6276 (pttt) cc_final: 0.5906 (tttt) outliers start: 24 outliers final: 5 residues processed: 121 average time/residue: 0.3431 time to fit residues: 45.0845 Evaluate side-chains 106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 316 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.093602 restraints weight = 8945.941| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.02 r_work: 0.2851 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.7720 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= 0.118 Angle : 0.511 6.649 10355 Z= 0.268 Chirality : 0.042 0.156 1177 Planarity : 0.003 0.035 1243 Dihedral : 14.138 101.150 1259 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.33 % Allowed : 20.40 % Favored : 76.27 % 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 are not related in a simple way. whole: 0.44 (0.28), residues: 940 helix: 1.73 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.85 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 497 TYR 0.008 0.001 TYR A 676 PHE 0.017 0.001 PHE A 387 TRP 0.013 0.001 TRP B 209 HIS 0.003 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7663) covalent geometry : angle 0.51109 / 0.27 (10351) SS BOND : bond 0.00625 / 0.33 ( 2) SS BOND : angle 0.88781 / 0.48 ( 4) hydrogen bonds : bond 0.03918 / 2.70 ( 428) hydrogen bonds : angle 3.51032 / 2.46 ( 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 122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.199 Fit side-chains REVERT: A 285 GLU cc_start: 0.8409 (pm20) cc_final: 0.8206 (pm20) REVERT: A 315 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: A 324 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.5994 (ttt) REVERT: A 381 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8293 (t) REVERT: A 634 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8420 (ttmt) REVERT: B 211 LYS cc_start: 0.9104 (tttm) cc_final: 0.8853 (tttm) REVERT: B 322 LEU cc_start: 0.7761 (mm) cc_final: 0.7462 (mm) REVERT: B 324 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6857 (pmm) REVERT: B 479 ILE cc_start: 0.5743 (OUTLIER) cc_final: 0.5097 (mm) REVERT: B 525 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8342 (p) REVERT: B 575 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7304 (pt0) outliers start: 25 outliers final: 4 residues processed: 117 average time/residue: 0.4104 time to fit residues: 51.5927 Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 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 381 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094182 restraints weight = 8962.684| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.95 r_work: 0.2866 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.7866 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= 0.108 Angle : 0.509 6.210 10355 Z= 0.265 Chirality : 0.041 0.165 1177 Planarity : 0.003 0.034 1243 Dihedral : 13.615 96.717 1258 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.40 % Allowed : 21.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 940 helix: 1.89 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.84 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.008 0.001 TYR B 676 PHE 0.013 0.001 PHE B 415 TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7663) covalent geometry : angle 0.50822 / 0.26 (10351) SS BOND : bond 0.00380 / 0.19 ( 2) SS BOND : angle 1.39073 / 0.77 ( 4) hydrogen bonds : bond 0.03651 / 2.52 ( 428) hydrogen bonds : angle 3.45677 / 2.42 ( 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 116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.282 Fit side-chains REVERT: A 285 GLU cc_start: 0.8331 (pm20) cc_final: 0.8119 (pm20) REVERT: A 315 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: A 324 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.5932 (ttt) REVERT: A 361 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7896 (tm) REVERT: A 381 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 499 THR cc_start: 0.7737 (p) cc_final: 0.7444 (m) REVERT: B 211 LYS cc_start: 0.9026 (tttm) cc_final: 0.8771 (tttm) REVERT: B 322 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (mm) REVERT: B 324 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6865 (pmm) REVERT: B 479 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5094 (mm) REVERT: B 525 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 575 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7238 (pt0) outliers start: 18 outliers final: 7 residues processed: 109 average time/residue: 0.4009 time to fit residues: 47.0803 Evaluate side-chains 104 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 B residue 307 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3420 r_free = 0.3420 target = 0.126882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095540 restraints weight = 9013.460| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.04 r_work: 0.2967 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.7985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7665 Z= 0.110 Angle : 0.512 9.008 10355 Z= 0.265 Chirality : 0.041 0.162 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.410 94.112 1258 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.67 % Allowed : 22.00 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.29), residues: 940 helix: 1.94 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.79 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.008 0.001 TYR B 676 PHE 0.015 0.001 PHE A 387 TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7663) covalent geometry : angle 0.51100 / 0.27 (10351) SS BOND : bond 0.00198 / 0.09 ( 2) SS BOND : angle 1.29055 / 0.71 ( 4) hydrogen bonds : bond 0.03746 / 2.58 ( 428) hydrogen bonds : angle 3.45713 / 2.41 ( 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 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.171 Fit side-chains REVERT: A 315 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: A 324 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.5839 (ttt) REVERT: A 361 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8016 (tm) REVERT: A 381 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8172 (t) REVERT: B 211 LYS cc_start: 0.9078 (tttm) cc_final: 0.8855 (tttm) REVERT: B 322 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7416 (mm) REVERT: B 324 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6957 (pmm) REVERT: B 525 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8469 (p) outliers start: 20 outliers final: 6 residues processed: 103 average time/residue: 0.3750 time to fit residues: 41.6475 Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 B residue 322 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 395 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 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: 3.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 35 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.0078 > 50:) chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 0.0020 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.096128 restraints weight = 8758.754| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.08 r_work: 0.2905 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7665 Z= 0.101 Angle : 0.509 12.144 10355 Z= 0.262 Chirality : 0.041 0.162 1177 Planarity : 0.003 0.032 1243 Dihedral : 13.068 89.508 1258 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.00 % Allowed : 22.53 % 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 are not related in a simple way. whole: 0.94 (0.29), residues: 940 helix: 2.09 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.69 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.006 0.001 TYR B 371 PHE 0.012 0.001 PHE B 415 TRP 0.012 0.001 TRP B 209 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 7663) covalent geometry : angle 0.50854 / 0.26 (10351) SS BOND : bond 0.00233 / 0.12 ( 2) SS BOND : angle 1.18061 / 0.65 ( 4) hydrogen bonds : bond 0.03518 / 2.43 ( 428) hydrogen bonds : angle 3.41170 / 2.39 ( 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 114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.194 Fit side-chains REVERT: A 315 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: A 324 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.5692 (ttt) REVERT: A 361 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8008 (tm) REVERT: A 381 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8120 (t) REVERT: A 634 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8424 (ttmt) REVERT: B 211 LYS cc_start: 0.9112 (tttm) cc_final: 0.8861 (tttm) REVERT: B 322 LEU cc_start: 0.7702 (mm) cc_final: 0.7441 (mm) REVERT: B 324 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6924 (pmm) REVERT: B 525 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 575 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7235 (pt0) outliers start: 15 outliers final: 6 residues processed: 109 average time/residue: 0.3520 time to fit residues: 41.4997 Evaluate side-chains 103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 634 LYS Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 395 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 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 49 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100601 restraints weight = 8803.093| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.91 r_work: 0.2861 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.8071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7665 Z= 0.149 Angle : 0.558 11.684 10355 Z= 0.288 Chirality : 0.043 0.162 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.468 94.658 1258 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.13 % Allowed : 22.80 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.28), residues: 940 helix: 1.84 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.74 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.009 0.001 TYR A 673 PHE 0.018 0.001 PHE A 387 TRP 0.011 0.002 TRP B 209 HIS 0.003 0.002 HIS B 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7663) covalent geometry : angle 0.55674 / 0.29 (10351) SS BOND : bond 0.00148 / 0.07 ( 2) SS BOND : angle 1.65727 / 0.88 ( 4) hydrogen bonds : bond 0.04213 / 2.90 ( 428) hydrogen bonds : angle 3.60128 / 2.51 ( 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 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.268 Fit side-chains REVERT: A 225 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.6323 (mpt) REVERT: A 361 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8090 (tm) REVERT: A 381 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8330 (t) REVERT: A 634 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8462 (ttmt) REVERT: B 211 LYS cc_start: 0.9090 (tttm) cc_final: 0.8887 (tttm) REVERT: B 322 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7475 (mm) REVERT: B 324 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7052 (pmm) REVERT: B 525 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8522 (p) outliers start: 16 outliers final: 7 residues processed: 92 average time/residue: 0.4243 time to fit residues: 41.9109 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 381 SER 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 395 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 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 76 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.095487 restraints weight = 8844.587| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.02 r_work: 0.2892 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.8154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7665 Z= 0.107 Angle : 0.520 11.292 10355 Z= 0.268 Chirality : 0.041 0.160 1177 Planarity : 0.003 0.033 1243 Dihedral : 13.014 88.399 1258 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.13 % Allowed : 22.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.29), residues: 940 helix: 2.05 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 310 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 0.013 0.001 PHE B 415 TRP 0.014 0.001 TRP B 209 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7663) covalent geometry : angle 0.51890 / 0.27 (10351) SS BOND : bond 0.00120 / 0.06 ( 2) SS BOND : angle 1.48787 / 0.80 ( 4) hydrogen bonds : bond 0.03632 / 2.50 ( 428) hydrogen bonds : angle 3.45191 / 2.42 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2206.27 seconds wall clock time: 38 minutes 26.22 seconds (2306.22 seconds total)