Starting phenix.real_space_refine on Fri Jun 5 10:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rux_54277/06_2026/9rux_54277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rux_54277/06_2026/9rux_54277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rux_54277/06_2026/9rux_54277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rux_54277/06_2026/9rux_54277.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rux_54277/06_2026/9rux_54277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rux_54277/06_2026/9rux_54277.map" } resolution = 3.9 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= 0.010 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 5960 2.51 5 N 1744 2.21 5 O 1820 1.98 5 H 9836 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19428 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4857 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain breaks: 1 Chain: "B" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4857 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain breaks: 1 Chain: "C" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4857 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4857 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain breaks: 1 Time building chain proxies: 3.58, per 1000 atoms: 0.18 Number of scatterers: 19428 At special positions: 0 Unit cell: (210.94, 83.74, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 1820 8.00 N 1744 7.00 C 5960 6.00 H 9836 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 634.7 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 91.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 327 through 369 Proline residue: A 336 - end of helix removed outlier: 3.762A pdb=" N LEU A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.939A pdb=" N ARG A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 419 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.741A pdb=" N ALA A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 530 removed outlier: 3.833A pdb=" N ALA A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 595 removed outlier: 4.303A pdb=" N GLU A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 598 through 678 removed outlier: 3.813A pdb=" N GLU A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 704 Processing helix chain 'B' and resid 327 through 369 Proline residue: B 336 - end of helix removed outlier: 3.836A pdb=" N LEU B 356 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 389 removed outlier: 3.859A pdb=" N ARG B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 419 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.749A pdb=" N ALA B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 530 removed outlier: 3.777A pdb=" N ALA B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 595 removed outlier: 4.287A pdb=" N GLU B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Proline residue: B 583 - end of helix Processing helix chain 'B' and resid 598 through 677 removed outlier: 3.795A pdb=" N GLU B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 704 Processing helix chain 'C' and resid 325 through 369 Proline residue: C 336 - end of helix removed outlier: 3.567A pdb=" N LEU C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 removed outlier: 3.522A pdb=" N ALA C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 380 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 419 removed outlier: 3.507A pdb=" N SER C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 Processing helix chain 'C' and resid 509 through 525 removed outlier: 4.240A pdb=" N GLY C 521 " --> pdb=" O SER C 517 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 595 Proline residue: C 583 - end of helix removed outlier: 3.507A pdb=" N SER C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 679 Processing helix chain 'C' and resid 681 through 704 removed outlier: 4.265A pdb=" N VAL C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 707 No H-bonds generated for 'chain 'C' and resid 705 through 707' Processing helix chain 'D' and resid 325 through 369 Proline residue: D 336 - end of helix removed outlier: 3.583A pdb=" N LEU D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 391 removed outlier: 3.578A pdb=" N ALA D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 419 removed outlier: 3.566A pdb=" N PHE D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 508 Processing helix chain 'D' and resid 509 through 524 removed outlier: 3.913A pdb=" N GLY D 521 " --> pdb=" O SER D 517 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 595 Proline residue: D 583 - end of helix Processing helix chain 'D' and resid 597 through 679 removed outlier: 3.540A pdb=" N ARG D 634 " --> pdb=" O SER D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 704 removed outlier: 4.232A pdb=" N VAL D 687 " --> pdb=" O LEU D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 707 No H-bonds generated for 'chain 'D' and resid 705 through 707' 911 hydrogen bonds defined for protein. 2733 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: 4.38 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9800 1.03 - 1.23: 45 1.23 - 1.42: 3820 1.42 - 1.62: 5779 1.62 - 1.81: 100 Bond restraints: 19544 Sorted by residual: bond pdb=" C CYS B 681 " pdb=" O CYS B 681 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.28e-02 6.10e+03 1.76e+01 bond pdb=" C CYS A 681 " pdb=" O CYS A 681 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.28e-02 6.10e+03 1.01e+01 bond pdb=" N LEU B 683 " pdb=" CA LEU B 683 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.18e+00 bond pdb=" N LEU A 683 " pdb=" CA LEU A 683 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.12e+00 bond pdb=" N ALA D 530 " pdb=" H ALA D 530 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.76e+00 ... (remaining 19539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 35297 2.50 - 4.99: 101 4.99 - 7.49: 13 7.49 - 9.98: 3 9.98 - 12.48: 2 Bond angle restraints: 35416 Sorted by residual: angle pdb=" N PRO B 682 " pdb=" CA PRO B 682 " pdb=" CB PRO B 682 " ideal model delta sigma weight residual 103.25 98.08 5.17 1.05e+00 9.07e-01 2.43e+01 angle pdb=" CA ALA D 530 " pdb=" C ALA D 530 " pdb=" O ALA D 530 " ideal model delta sigma weight residual 120.16 114.21 5.95 1.37e+00 5.33e-01 1.89e+01 angle pdb=" N PRO A 682 " pdb=" CA PRO A 682 " pdb=" CB PRO A 682 " ideal model delta sigma weight residual 103.25 98.83 4.42 1.05e+00 9.07e-01 1.77e+01 angle pdb=" N PHE C 532 " pdb=" CA PHE C 532 " pdb=" C PHE C 532 " ideal model delta sigma weight residual 114.75 109.65 5.10 1.26e+00 6.30e-01 1.64e+01 angle pdb=" CA CYS B 681 " pdb=" C CYS B 681 " pdb=" O CYS B 681 " ideal model delta sigma weight residual 120.16 114.67 5.49 1.37e+00 5.33e-01 1.61e+01 ... (remaining 35411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 8379 16.63 - 33.26: 430 33.26 - 49.88: 111 49.88 - 66.51: 83 66.51 - 83.14: 13 Dihedral angle restraints: 9016 sinusoidal: 5160 harmonic: 3856 Sorted by residual: dihedral pdb=" CA ALA C 530 " pdb=" C ALA C 530 " pdb=" N PRO C 531 " pdb=" CA PRO C 531 " ideal model delta harmonic sigma weight residual -180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA CYS C 597 " pdb=" C CYS C 597 " pdb=" N PHE C 598 " pdb=" CA PHE C 598 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA TRP C 393 " pdb=" C TRP C 393 " pdb=" N ALA C 394 " pdb=" CA ALA C 394 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1323 0.045 - 0.090: 172 0.090 - 0.134: 19 0.134 - 0.179: 0 0.179 - 0.224: 2 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA ALA D 530 " pdb=" N ALA D 530 " pdb=" C ALA D 530 " pdb=" CB ALA D 530 " both_signs ideal model delta sigma weight residual False 2.48 2.71 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PRO C 531 " pdb=" N PRO C 531 " pdb=" C PRO C 531 " pdb=" CB PRO C 531 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA PHE D 532 " pdb=" N PHE D 532 " pdb=" C PHE D 532 " pdb=" CB PHE D 532 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 1513 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 530 " 0.096 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO C 531 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO C 531 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO C 531 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 681 " -0.023 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C CYS B 681 " 0.080 2.00e-02 2.50e+03 pdb=" O CYS B 681 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO B 682 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 681 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C CYS A 681 " -0.072 2.00e-02 2.50e+03 pdb=" O CYS A 681 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO A 682 " 0.025 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 888 2.20 - 2.80: 40641 2.80 - 3.40: 53348 3.40 - 4.00: 61264 4.00 - 4.60: 99497 Nonbonded interactions: 255638 Sorted by model distance: nonbonded pdb=" OE1 GLN B 507 " pdb=" H GLN B 507 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP A 579 " pdb=" HE ARG A 615 " model vdw 1.603 2.450 nonbonded pdb=" O GLN B 675 " pdb=" HG SER B 678 " model vdw 1.605 2.450 nonbonded pdb=" OD1 ASP B 579 " pdb=" HE ARG B 615 " model vdw 1.614 2.450 nonbonded pdb=" O ALA C 324 " pdb=" H HIS C 328 " model vdw 1.636 2.450 ... (remaining 255633 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 324 through 417 or (resid 418 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 419 through 707)) selection = (chain 'B' and (resid 324 through 417 or (resid 418 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 419 through 707)) selection = (chain 'C' and (resid 324 through 656 or (resid 657 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 658 through 707)) selection = (chain 'D' and (resid 324 through 656 or (resid 657 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 658 through 707)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.240 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.750 Find NCS groups from input model: 0.280 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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 : 0.005 0.054 9708 Z= 0.245 Angle : 0.606 8.638 13076 Z= 0.364 Chirality : 0.031 0.224 1516 Planarity : 0.005 0.144 1684 Dihedral : 11.368 83.141 3772 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.67 % Favored : 97.83 % Rotamer: Outliers : 0.28 % Allowed : 2.56 % Favored : 97.16 % 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: 3.50 (0.23), residues: 1200 helix: 2.73 (0.15), residues: 1006 sheet: None (None), residues: 0 loop : -0.01 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 403 TYR 0.006 0.001 TYR B 341 PHE 0.017 0.002 PHE C 621 TRP 0.010 0.001 TRP C 393 HIS 0.004 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.24 ( 9708) covalent geometry : angle 0.60607 / 0.36 (13076) hydrogen bonds : bond 0.09759 / 6.72 ( 911) hydrogen bonds : angle 4.50376 / 3.24 ( 2733) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7672 (tt0) cc_final: 0.7032 (tt0) REVERT: A 334 TRP cc_start: 0.7633 (m100) cc_final: 0.6962 (m100) REVERT: A 336 PRO cc_start: 0.8976 (Cg_exo) cc_final: 0.8767 (Cg_endo) REVERT: A 350 GLU cc_start: 0.7858 (tt0) cc_final: 0.7649 (tp30) REVERT: A 360 LYS cc_start: 0.8281 (tttt) cc_final: 0.7917 (ttmm) REVERT: A 520 LEU cc_start: 0.8513 (mt) cc_final: 0.8158 (mt) REVERT: A 533 GLN cc_start: 0.8175 (pp30) cc_final: 0.7895 (pp30) REVERT: A 577 ASP cc_start: 0.7333 (m-30) cc_final: 0.7006 (t0) REVERT: A 647 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7421 (ttm-80) REVERT: A 660 ARG cc_start: 0.6925 (ttp-110) cc_final: 0.6549 (mtm110) REVERT: A 680 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7507 (mpp-170) REVERT: A 689 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8253 (ttmm) REVERT: B 360 LYS cc_start: 0.8257 (tttt) cc_final: 0.7968 (ttmm) REVERT: B 544 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7979 (ttm170) REVERT: B 577 ASP cc_start: 0.7230 (m-30) cc_final: 0.6905 (t0) REVERT: B 689 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8239 (mtmm) REVERT: C 337 MET cc_start: 0.8422 (mpp) cc_final: 0.8014 (mmm) REVERT: C 350 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6922 (mm-30) REVERT: C 357 LYS cc_start: 0.8150 (tptm) cc_final: 0.7771 (tptm) REVERT: C 370 ASP cc_start: 0.7104 (t0) cc_final: 0.6579 (t0) REVERT: C 518 LYS cc_start: 0.8688 (ptmt) cc_final: 0.8484 (pttm) REVERT: C 541 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7493 (ttp-170) REVERT: C 658 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8385 (tppp) REVERT: C 665 THR cc_start: 0.7839 (m) cc_final: 0.7291 (m) REVERT: C 666 VAL cc_start: 0.8505 (t) cc_final: 0.8078 (t) REVERT: C 669 MET cc_start: 0.7801 (mtp) cc_final: 0.7391 (mtp) REVERT: D 357 LYS cc_start: 0.7985 (tptm) cc_final: 0.7545 (tptm) REVERT: D 370 ASP cc_start: 0.7057 (t0) cc_final: 0.6601 (t0) REVERT: D 373 THR cc_start: 0.7336 (p) cc_final: 0.6879 (p) REVERT: D 414 GLN cc_start: 0.7709 (tp40) cc_final: 0.7265 (tp40) REVERT: D 541 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7572 (ttp80) REVERT: D 590 MET cc_start: 0.8400 (tpp) cc_final: 0.7995 (tpp) REVERT: D 635 ARG cc_start: 0.7880 (ttt180) cc_final: 0.7590 (mmm-85) REVERT: D 654 ASP cc_start: 0.7704 (m-30) cc_final: 0.7393 (m-30) REVERT: D 665 THR cc_start: 0.7802 (m) cc_final: 0.7201 (m) REVERT: D 666 VAL cc_start: 0.8437 (t) cc_final: 0.7968 (t) REVERT: D 669 MET cc_start: 0.7660 (mtp) cc_final: 0.7238 (mtp) outliers start: 3 outliers final: 2 residues processed: 351 average time/residue: 0.3569 time to fit residues: 155.6168 Evaluate side-chains 315 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 682 PRO Chi-restraints excluded: chain C residue 677 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 GLN C 348 GLN D 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121770 restraints weight = 48893.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126952 restraints weight = 19704.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129879 restraints weight = 9670.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131520 restraints weight = 5557.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132605 restraints weight = 3765.340| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9708 Z= 0.176 Angle : 0.557 9.938 13076 Z= 0.303 Chirality : 0.030 0.196 1516 Planarity : 0.005 0.143 1684 Dihedral : 4.060 28.463 1324 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.08 % Favored : 98.67 % Rotamer: Outliers : 1.04 % Allowed : 9.94 % Favored : 89.02 % 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: 3.81 (0.23), residues: 1200 helix: 2.86 (0.15), residues: 1014 sheet: None (None), residues: 0 loop : 0.47 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 634 TYR 0.005 0.001 TYR D 408 PHE 0.031 0.002 PHE D 532 TRP 0.008 0.001 TRP A 334 HIS 0.005 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 ( 9708) covalent geometry : angle 0.55707 / 0.30 (13076) hydrogen bonds : bond 0.05567 / 3.70 ( 911) hydrogen bonds : angle 4.02508 / 2.92 ( 2733) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 320 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7434 (tt0) cc_final: 0.6911 (tt0) REVERT: A 334 TRP cc_start: 0.7422 (m100) cc_final: 0.6546 (m100) REVERT: A 360 LYS cc_start: 0.8320 (tttt) cc_final: 0.7964 (ttmm) REVERT: A 577 ASP cc_start: 0.7297 (m-30) cc_final: 0.7042 (t0) REVERT: A 581 ARG cc_start: 0.7374 (mtp85) cc_final: 0.6930 (mtp-110) REVERT: A 660 ARG cc_start: 0.6950 (ttp-110) cc_final: 0.6619 (mtm110) REVERT: A 684 LEU cc_start: 0.7718 (tp) cc_final: 0.7458 (tp) REVERT: A 689 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8157 (ttmm) REVERT: B 354 LEU cc_start: 0.8290 (tp) cc_final: 0.8008 (tt) REVERT: B 360 LYS cc_start: 0.8288 (tttt) cc_final: 0.8013 (ttmm) REVERT: B 405 PHE cc_start: 0.8541 (t80) cc_final: 0.8271 (t80) REVERT: B 544 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7954 (ttm170) REVERT: B 577 ASP cc_start: 0.7099 (m-30) cc_final: 0.6887 (t0) REVERT: B 602 LYS cc_start: 0.7534 (ttmm) cc_final: 0.7301 (ttmm) REVERT: B 673 GLU cc_start: 0.7410 (tp30) cc_final: 0.7024 (tp30) REVERT: B 689 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8100 (mtmm) REVERT: C 337 MET cc_start: 0.8234 (mpp) cc_final: 0.7863 (mmm) REVERT: C 357 LYS cc_start: 0.8148 (tptm) cc_final: 0.7781 (tptm) REVERT: C 367 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 370 ASP cc_start: 0.6847 (t0) cc_final: 0.6419 (t0) REVERT: C 373 THR cc_start: 0.7609 (p) cc_final: 0.7093 (p) REVERT: C 385 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7190 (mt-10) REVERT: C 658 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8383 (tppp) REVERT: C 665 THR cc_start: 0.7809 (m) cc_final: 0.7154 (m) REVERT: C 669 MET cc_start: 0.7555 (mtp) cc_final: 0.7235 (mtp) REVERT: D 357 LYS cc_start: 0.7930 (tptm) cc_final: 0.7523 (tptm) REVERT: D 370 ASP cc_start: 0.6721 (t0) cc_final: 0.6308 (t0) REVERT: D 373 THR cc_start: 0.7463 (p) cc_final: 0.6881 (p) REVERT: D 414 GLN cc_start: 0.7435 (tp40) cc_final: 0.7010 (tp40) REVERT: D 500 ASP cc_start: 0.7638 (t0) cc_final: 0.7218 (t70) REVERT: D 502 MET cc_start: 0.7586 (ptt) cc_final: 0.7216 (ptt) REVERT: D 590 MET cc_start: 0.7988 (tpp) cc_final: 0.7553 (tpp) REVERT: D 620 MET cc_start: 0.4643 (tmm) cc_final: 0.4333 (tmm) REVERT: D 635 ARG cc_start: 0.7839 (ttt180) cc_final: 0.7621 (mmm-85) REVERT: D 654 ASP cc_start: 0.7672 (m-30) cc_final: 0.7293 (m-30) REVERT: D 665 THR cc_start: 0.7767 (m) cc_final: 0.7032 (m) REVERT: D 666 VAL cc_start: 0.8407 (t) cc_final: 0.7900 (t) REVERT: D 669 MET cc_start: 0.7460 (mtp) cc_final: 0.7128 (mtp) outliers start: 11 outliers final: 11 residues processed: 322 average time/residue: 0.3667 time to fit residues: 146.2587 Evaluate side-chains 326 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 533 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120011 restraints weight = 49040.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125185 restraints weight = 19953.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128202 restraints weight = 9885.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129949 restraints weight = 5714.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130954 restraints weight = 3791.195| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9708 Z= 0.218 Angle : 0.565 10.615 13076 Z= 0.312 Chirality : 0.031 0.198 1516 Planarity : 0.005 0.141 1684 Dihedral : 3.989 29.607 1320 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.50 % Favored : 98.25 % Rotamer: Outliers : 1.42 % Allowed : 12.41 % Favored : 86.17 % 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: 3.71 (0.23), residues: 1200 helix: 2.81 (0.15), residues: 1014 sheet: None (None), residues: 0 loop : 0.31 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 581 TYR 0.004 0.001 TYR B 341 PHE 0.033 0.002 PHE D 532 TRP 0.009 0.001 TRP A 334 HIS 0.005 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.22 ( 9708) covalent geometry : angle 0.56470 / 0.31 (13076) hydrogen bonds : bond 0.05517 / 3.66 ( 911) hydrogen bonds : angle 4.02858 / 2.94 ( 2733) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7529 (tt0) cc_final: 0.7019 (tt0) REVERT: A 334 TRP cc_start: 0.7455 (m100) cc_final: 0.6607 (m100) REVERT: A 360 LYS cc_start: 0.8304 (tttt) cc_final: 0.7952 (ttmm) REVERT: A 533 GLN cc_start: 0.8158 (pp30) cc_final: 0.7584 (pp30) REVERT: A 577 ASP cc_start: 0.7310 (m-30) cc_final: 0.7059 (t0) REVERT: A 660 ARG cc_start: 0.6838 (ttp-110) cc_final: 0.6440 (mtm180) REVERT: A 673 GLU cc_start: 0.7359 (tp30) cc_final: 0.6701 (tp30) REVERT: A 684 LEU cc_start: 0.7800 (tp) cc_final: 0.7549 (tp) REVERT: A 689 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8195 (ttmm) REVERT: B 354 LEU cc_start: 0.8315 (tp) cc_final: 0.8042 (tt) REVERT: B 360 LYS cc_start: 0.8293 (tttt) cc_final: 0.7995 (ttmm) REVERT: B 405 PHE cc_start: 0.8612 (t80) cc_final: 0.8399 (t80) REVERT: B 577 ASP cc_start: 0.7112 (m-30) cc_final: 0.6898 (t0) REVERT: B 673 GLU cc_start: 0.7545 (tp30) cc_final: 0.7122 (tp30) REVERT: B 675 GLN cc_start: 0.8156 (mp10) cc_final: 0.7858 (mp10) REVERT: B 689 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8203 (mtmm) REVERT: C 337 MET cc_start: 0.8292 (mpp) cc_final: 0.7934 (mmp) REVERT: C 370 ASP cc_start: 0.6903 (t0) cc_final: 0.6464 (t0) REVERT: C 373 THR cc_start: 0.7638 (p) cc_final: 0.7117 (p) REVERT: C 385 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 402 LEU cc_start: 0.8686 (mp) cc_final: 0.8426 (tt) REVERT: C 541 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7231 (ttp-110) REVERT: C 658 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8402 (tppp) REVERT: C 665 THR cc_start: 0.7877 (m) cc_final: 0.7236 (m) REVERT: C 669 MET cc_start: 0.7608 (mtp) cc_final: 0.7261 (mtp) REVERT: D 357 LYS cc_start: 0.7976 (tptm) cc_final: 0.7558 (tptm) REVERT: D 370 ASP cc_start: 0.6829 (t0) cc_final: 0.6404 (t0) REVERT: D 373 THR cc_start: 0.7502 (p) cc_final: 0.6951 (p) REVERT: D 414 GLN cc_start: 0.7527 (tp40) cc_final: 0.7083 (tp40) REVERT: D 590 MET cc_start: 0.7955 (tpp) cc_final: 0.7541 (tpp) REVERT: D 620 MET cc_start: 0.4721 (tmm) cc_final: 0.4389 (tmm) REVERT: D 635 ARG cc_start: 0.7806 (ttt180) cc_final: 0.7542 (mmm-85) REVERT: D 654 ASP cc_start: 0.7726 (m-30) cc_final: 0.7332 (m-30) REVERT: D 665 THR cc_start: 0.7825 (m) cc_final: 0.7097 (m) REVERT: D 669 MET cc_start: 0.7507 (mtp) cc_final: 0.7149 (mtp) outliers start: 15 outliers final: 12 residues processed: 322 average time/residue: 0.3564 time to fit residues: 143.2977 Evaluate side-chains 321 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 309 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 533 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN C 379 GLN D 675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113851 restraints weight = 48721.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.119209 restraints weight = 20230.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122032 restraints weight = 10206.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124003 restraints weight = 6245.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125039 restraints weight = 4131.969| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9708 Z= 0.246 Angle : 0.579 10.529 13076 Z= 0.321 Chirality : 0.032 0.197 1516 Planarity : 0.005 0.140 1684 Dihedral : 4.051 30.556 1320 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.67 % Favored : 98.08 % Rotamer: Outliers : 2.18 % Allowed : 14.20 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 3.56 (0.23), residues: 1200 helix: 2.75 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -0.07 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 572 TYR 0.008 0.001 TYR C 371 PHE 0.034 0.003 PHE D 532 TRP 0.009 0.001 TRP C 393 HIS 0.006 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.25 ( 9708) covalent geometry : angle 0.57888 / 0.32 (13076) hydrogen bonds : bond 0.05554 / 3.68 ( 911) hydrogen bonds : angle 4.08518 / 3.00 ( 2733) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 315 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7528 (tt0) cc_final: 0.7054 (tt0) REVERT: A 334 TRP cc_start: 0.7356 (m100) cc_final: 0.6469 (m100) REVERT: A 360 LYS cc_start: 0.8292 (tttt) cc_final: 0.7980 (ttmm) REVERT: A 533 GLN cc_start: 0.8191 (pp30) cc_final: 0.7944 (pp30) REVERT: A 577 ASP cc_start: 0.7308 (m-30) cc_final: 0.7092 (t0) REVERT: A 581 ARG cc_start: 0.7297 (mtp85) cc_final: 0.6751 (mtp-110) REVERT: A 660 ARG cc_start: 0.6859 (ttp-110) cc_final: 0.6506 (mtm180) REVERT: A 684 LEU cc_start: 0.7818 (tp) cc_final: 0.7570 (tp) REVERT: A 689 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8208 (ttmm) REVERT: A 699 MET cc_start: 0.7476 (tpp) cc_final: 0.7269 (tpt) REVERT: B 354 LEU cc_start: 0.8309 (tp) cc_final: 0.8046 (tt) REVERT: B 360 LYS cc_start: 0.8332 (tttt) cc_final: 0.8032 (ttmm) REVERT: B 577 ASP cc_start: 0.7153 (m-30) cc_final: 0.6919 (t0) REVERT: B 673 GLU cc_start: 0.7487 (tp30) cc_final: 0.7092 (tp30) REVERT: B 675 GLN cc_start: 0.8132 (mp10) cc_final: 0.7797 (mp10) REVERT: B 689 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8201 (mtmm) REVERT: C 337 MET cc_start: 0.8294 (mpp) cc_final: 0.7952 (mmp) REVERT: C 370 ASP cc_start: 0.6857 (t0) cc_final: 0.6506 (t0) REVERT: C 373 THR cc_start: 0.7679 (p) cc_final: 0.7190 (p) REVERT: C 385 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7239 (mt-10) REVERT: C 541 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7180 (ttp-110) REVERT: C 658 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8411 (tppp) REVERT: C 665 THR cc_start: 0.7884 (m) cc_final: 0.7222 (m) REVERT: C 669 MET cc_start: 0.7638 (mtp) cc_final: 0.7235 (mtp) REVERT: D 357 LYS cc_start: 0.8021 (tptm) cc_final: 0.7604 (tptm) REVERT: D 370 ASP cc_start: 0.6904 (t0) cc_final: 0.6503 (t0) REVERT: D 373 THR cc_start: 0.7544 (p) cc_final: 0.7000 (p) REVERT: D 414 GLN cc_start: 0.7541 (tp40) cc_final: 0.7095 (tp40) REVERT: D 590 MET cc_start: 0.7991 (tpp) cc_final: 0.7564 (tpp) REVERT: D 620 MET cc_start: 0.4668 (tmm) cc_final: 0.4369 (tmm) REVERT: D 635 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7577 (mmm-85) outliers start: 23 outliers final: 21 residues processed: 327 average time/residue: 0.3482 time to fit residues: 141.9766 Evaluate side-chains 333 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 312 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 533 GLN Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 677 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.133878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114835 restraints weight = 48797.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120308 restraints weight = 20323.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123350 restraints weight = 10160.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125191 restraints weight = 5954.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126282 restraints weight = 4029.116| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9708 Z= 0.179 Angle : 0.543 10.200 13076 Z= 0.292 Chirality : 0.029 0.189 1516 Planarity : 0.005 0.137 1684 Dihedral : 3.964 30.608 1320 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.67 % Favored : 98.08 % Rotamer: Outliers : 1.89 % Allowed : 15.15 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 3.82 (0.23), residues: 1200 helix: 2.94 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : 0.08 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 635 TYR 0.004 0.001 TYR C 371 PHE 0.032 0.002 PHE D 532 TRP 0.009 0.001 TRP A 334 HIS 0.003 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 ( 9708) covalent geometry : angle 0.54325 / 0.29 (13076) hydrogen bonds : bond 0.05308 / 3.51 ( 911) hydrogen bonds : angle 3.87173 / 2.84 ( 2733) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7463 (tt0) cc_final: 0.7015 (tt0) REVERT: A 334 TRP cc_start: 0.7279 (m100) cc_final: 0.6453 (m100) REVERT: A 360 LYS cc_start: 0.8283 (tttt) cc_final: 0.7952 (ttmm) REVERT: A 533 GLN cc_start: 0.8204 (pp30) cc_final: 0.7952 (pp30) REVERT: A 577 ASP cc_start: 0.7293 (m-30) cc_final: 0.7035 (t0) REVERT: A 660 ARG cc_start: 0.6836 (ttp-110) cc_final: 0.6532 (mtm180) REVERT: A 675 GLN cc_start: 0.8074 (mp10) cc_final: 0.7810 (mp10) REVERT: A 684 LEU cc_start: 0.7765 (tp) cc_final: 0.7525 (tp) REVERT: A 689 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8215 (ttmm) REVERT: B 354 LEU cc_start: 0.8276 (tp) cc_final: 0.8012 (tt) REVERT: B 360 LYS cc_start: 0.8324 (tttt) cc_final: 0.8019 (ttmm) REVERT: B 405 PHE cc_start: 0.8649 (t80) cc_final: 0.8442 (t80) REVERT: B 545 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7128 (tm-30) REVERT: B 577 ASP cc_start: 0.7126 (m-30) cc_final: 0.6907 (t0) REVERT: B 673 GLU cc_start: 0.7492 (tp30) cc_final: 0.7045 (tp30) REVERT: B 675 GLN cc_start: 0.8131 (mp10) cc_final: 0.7776 (mp10) REVERT: B 689 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8187 (mtmm) REVERT: C 335 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8650 (tm-30) REVERT: C 337 MET cc_start: 0.8285 (mpp) cc_final: 0.7952 (mmp) REVERT: C 370 ASP cc_start: 0.6891 (t0) cc_final: 0.6549 (t0) REVERT: C 373 THR cc_start: 0.7584 (p) cc_final: 0.7105 (p) REVERT: C 385 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7267 (mt-10) REVERT: C 541 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7183 (ttp-110) REVERT: C 640 LYS cc_start: 0.7657 (tttt) cc_final: 0.7365 (ttmm) REVERT: C 658 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8399 (tppp) REVERT: C 665 THR cc_start: 0.7888 (m) cc_final: 0.7205 (m) REVERT: C 669 MET cc_start: 0.7638 (mtp) cc_final: 0.7218 (mtp) REVERT: D 357 LYS cc_start: 0.8012 (tptm) cc_final: 0.7599 (tptm) REVERT: D 370 ASP cc_start: 0.6903 (t0) cc_final: 0.6518 (t0) REVERT: D 373 THR cc_start: 0.7441 (p) cc_final: 0.6928 (p) REVERT: D 414 GLN cc_start: 0.7554 (tp40) cc_final: 0.7095 (tp40) REVERT: D 545 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7539 (tm-30) REVERT: D 590 MET cc_start: 0.7957 (tpp) cc_final: 0.7499 (tpp) REVERT: D 620 MET cc_start: 0.4722 (tmm) cc_final: 0.4408 (tmm) outliers start: 20 outliers final: 16 residues processed: 320 average time/residue: 0.3558 time to fit residues: 141.3988 Evaluate side-chains 319 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 303 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 533 GLN Chi-restraints excluded: chain D residue 593 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 103 optimal weight: 0.0040 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113964 restraints weight = 48274.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.119350 restraints weight = 20061.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122426 restraints weight = 10103.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124178 restraints weight = 5921.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125243 restraints weight = 4065.953| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9708 Z= 0.223 Angle : 0.566 10.178 13076 Z= 0.309 Chirality : 0.031 0.192 1516 Planarity : 0.005 0.136 1684 Dihedral : 3.999 30.844 1320 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.83 % Favored : 97.92 % Rotamer: Outliers : 1.89 % Allowed : 15.34 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 3.66 (0.23), residues: 1200 helix: 2.81 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : 0.04 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 581 TYR 0.006 0.001 TYR C 371 PHE 0.031 0.002 PHE D 532 TRP 0.014 0.001 TRP C 334 HIS 0.006 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 ( 9708) covalent geometry : angle 0.56572 / 0.31 (13076) hydrogen bonds : bond 0.05382 / 3.56 ( 911) hydrogen bonds : angle 3.96560 / 2.92 ( 2733) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7502 (tt0) cc_final: 0.7087 (tt0) REVERT: A 334 TRP cc_start: 0.7133 (m100) cc_final: 0.6354 (m100) REVERT: A 360 LYS cc_start: 0.8306 (tttt) cc_final: 0.7985 (ttmm) REVERT: A 577 ASP cc_start: 0.7298 (m-30) cc_final: 0.7061 (t0) REVERT: A 607 GLU cc_start: 0.7095 (tt0) cc_final: 0.6761 (tt0) REVERT: A 675 GLN cc_start: 0.8073 (mp10) cc_final: 0.7816 (mp10) REVERT: A 689 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8236 (ttmm) REVERT: B 354 LEU cc_start: 0.8302 (tp) cc_final: 0.8046 (tt) REVERT: B 360 LYS cc_start: 0.8348 (tttt) cc_final: 0.8033 (ttmm) REVERT: B 577 ASP cc_start: 0.7154 (m-30) cc_final: 0.6930 (t0) REVERT: B 673 GLU cc_start: 0.7453 (tp30) cc_final: 0.7072 (tp30) REVERT: B 675 GLN cc_start: 0.8132 (mp10) cc_final: 0.7801 (mp10) REVERT: B 689 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8205 (mtmm) REVERT: C 335 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8635 (tm-30) REVERT: C 337 MET cc_start: 0.8271 (mpp) cc_final: 0.7933 (mmp) REVERT: C 370 ASP cc_start: 0.6955 (t0) cc_final: 0.6610 (t0) REVERT: C 373 THR cc_start: 0.7678 (p) cc_final: 0.7186 (p) REVERT: C 402 LEU cc_start: 0.8868 (tp) cc_final: 0.8627 (tp) REVERT: C 541 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7228 (ttp-110) REVERT: C 658 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8412 (tppp) REVERT: C 665 THR cc_start: 0.7877 (m) cc_final: 0.7198 (m) REVERT: C 669 MET cc_start: 0.7611 (mtp) cc_final: 0.7213 (mtp) REVERT: D 357 LYS cc_start: 0.8035 (tptm) cc_final: 0.7629 (tptm) REVERT: D 370 ASP cc_start: 0.6949 (t0) cc_final: 0.6548 (t0) REVERT: D 373 THR cc_start: 0.7550 (p) cc_final: 0.7036 (p) REVERT: D 414 GLN cc_start: 0.7521 (tp40) cc_final: 0.7072 (tp40) REVERT: D 545 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7487 (tm-30) REVERT: D 590 MET cc_start: 0.7991 (tpp) cc_final: 0.7529 (tpp) REVERT: D 620 MET cc_start: 0.4695 (tmm) cc_final: 0.4423 (tmm) REVERT: D 658 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8380 (tppp) REVERT: D 669 MET cc_start: 0.7494 (mtp) cc_final: 0.7124 (mtp) outliers start: 20 outliers final: 16 residues processed: 314 average time/residue: 0.3386 time to fit residues: 132.7162 Evaluate side-chains 318 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 302 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 593 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 109 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113342 restraints weight = 48362.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118753 restraints weight = 20129.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121789 restraints weight = 10154.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123587 restraints weight = 5964.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.124352 restraints weight = 4054.164| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9708 Z= 0.244 Angle : 0.580 10.752 13076 Z= 0.319 Chirality : 0.032 0.194 1516 Planarity : 0.006 0.135 1684 Dihedral : 4.046 31.230 1320 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.25 % Favored : 97.50 % Rotamer: Outliers : 1.89 % Allowed : 16.10 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 3.56 (0.23), residues: 1200 helix: 2.80 (0.15), residues: 1002 sheet: None (None), residues: 0 loop : -0.15 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 634 TYR 0.008 0.001 TYR C 371 PHE 0.031 0.003 PHE D 532 TRP 0.009 0.001 TRP A 334 HIS 0.004 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.24 ( 9708) covalent geometry : angle 0.58003 / 0.32 (13076) hydrogen bonds : bond 0.05455 / 3.60 ( 911) hydrogen bonds : angle 4.02329 / 2.96 ( 2733) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 305 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7525 (tt0) cc_final: 0.7104 (tt0) REVERT: A 334 TRP cc_start: 0.7156 (m100) cc_final: 0.6332 (m100) REVERT: A 360 LYS cc_start: 0.8318 (tttt) cc_final: 0.7990 (ttmm) REVERT: A 577 ASP cc_start: 0.7300 (m-30) cc_final: 0.7093 (t0) REVERT: A 607 GLU cc_start: 0.7143 (tt0) cc_final: 0.6798 (tt0) REVERT: A 675 GLN cc_start: 0.8085 (mp10) cc_final: 0.7813 (mp10) REVERT: A 689 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8246 (ttmm) REVERT: B 354 LEU cc_start: 0.8304 (tp) cc_final: 0.8052 (tt) REVERT: B 360 LYS cc_start: 0.8355 (tttt) cc_final: 0.8040 (ttmm) REVERT: B 577 ASP cc_start: 0.7160 (m-30) cc_final: 0.6937 (t0) REVERT: B 673 GLU cc_start: 0.7462 (tp30) cc_final: 0.7080 (tp30) REVERT: B 675 GLN cc_start: 0.8147 (mp10) cc_final: 0.7815 (mp10) REVERT: B 689 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8174 (mtmm) REVERT: C 335 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8623 (tm-30) REVERT: C 337 MET cc_start: 0.8278 (mpp) cc_final: 0.7942 (mmp) REVERT: C 370 ASP cc_start: 0.6980 (t0) cc_final: 0.6646 (t0) REVERT: C 373 THR cc_start: 0.7716 (p) cc_final: 0.7234 (p) REVERT: C 402 LEU cc_start: 0.8884 (tp) cc_final: 0.8650 (tp) REVERT: C 541 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7210 (ttp-110) REVERT: C 645 ARG cc_start: 0.6968 (tpp80) cc_final: 0.6685 (tpp-160) REVERT: C 658 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8376 (tppp) REVERT: C 665 THR cc_start: 0.7881 (m) cc_final: 0.7208 (m) REVERT: C 669 MET cc_start: 0.7644 (mtp) cc_final: 0.7229 (mtp) REVERT: D 357 LYS cc_start: 0.8041 (tptm) cc_final: 0.7646 (tptm) REVERT: D 370 ASP cc_start: 0.7039 (t0) cc_final: 0.6692 (t0) REVERT: D 373 THR cc_start: 0.7576 (p) cc_final: 0.7076 (p) REVERT: D 414 GLN cc_start: 0.7524 (tp40) cc_final: 0.7068 (tp40) REVERT: D 545 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7487 (tm-30) REVERT: D 590 MET cc_start: 0.7958 (tpp) cc_final: 0.7520 (tpp) REVERT: D 620 MET cc_start: 0.4547 (tmm) cc_final: 0.4271 (tmm) REVERT: D 658 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8385 (tppp) REVERT: D 669 MET cc_start: 0.7500 (mtp) cc_final: 0.7243 (mtp) outliers start: 20 outliers final: 18 residues processed: 318 average time/residue: 0.3448 time to fit residues: 136.6697 Evaluate side-chains 320 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 302 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 533 GLN Chi-restraints excluded: chain D residue 593 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 0.0980 chunk 4 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 13 optimal weight: 0.0270 chunk 110 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 118 optimal weight: 0.0980 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116080 restraints weight = 48534.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121553 restraints weight = 20168.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124676 restraints weight = 10047.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126407 restraints weight = 5835.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127502 restraints weight = 4006.156| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9708 Z= 0.126 Angle : 0.525 10.295 13076 Z= 0.272 Chirality : 0.028 0.179 1516 Planarity : 0.005 0.133 1684 Dihedral : 3.834 30.669 1320 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.25 % Favored : 98.50 % Rotamer: Outliers : 1.52 % Allowed : 16.48 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 4.19 (0.24), residues: 1200 helix: 3.18 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : 0.29 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 634 TYR 0.003 0.001 TYR B 371 PHE 0.028 0.002 PHE D 532 TRP 0.009 0.001 TRP A 334 HIS 0.002 0.001 HIS D 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9708) covalent geometry : angle 0.52477 / 0.27 (13076) hydrogen bonds : bond 0.04977 / 3.29 ( 911) hydrogen bonds : angle 3.61226 / 2.65 ( 2733) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 304 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7408 (tt0) cc_final: 0.6976 (tt0) REVERT: A 334 TRP cc_start: 0.7055 (m100) cc_final: 0.6312 (m100) REVERT: A 360 LYS cc_start: 0.8286 (tttt) cc_final: 0.7936 (tppt) REVERT: A 533 GLN cc_start: 0.8070 (pp30) cc_final: 0.7417 (pp30) REVERT: A 577 ASP cc_start: 0.7266 (m-30) cc_final: 0.6902 (t70) REVERT: A 607 GLU cc_start: 0.7167 (tt0) cc_final: 0.6744 (tt0) REVERT: A 675 GLN cc_start: 0.8067 (mp10) cc_final: 0.7769 (mp10) REVERT: A 689 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8188 (ttmm) REVERT: B 354 LEU cc_start: 0.8244 (tp) cc_final: 0.8000 (tt) REVERT: B 360 LYS cc_start: 0.8329 (tttt) cc_final: 0.8017 (ttmm) REVERT: B 405 PHE cc_start: 0.8621 (t80) cc_final: 0.8376 (t80) REVERT: B 577 ASP cc_start: 0.7164 (m-30) cc_final: 0.6952 (t0) REVERT: B 641 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7219 (tp30) REVERT: B 673 GLU cc_start: 0.7405 (tp30) cc_final: 0.6973 (tp30) REVERT: B 675 GLN cc_start: 0.8111 (mp10) cc_final: 0.7735 (mp10) REVERT: B 689 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8134 (mtmm) REVERT: C 337 MET cc_start: 0.8259 (mpp) cc_final: 0.7888 (mmp) REVERT: C 370 ASP cc_start: 0.6925 (t0) cc_final: 0.6489 (t0) REVERT: C 402 LEU cc_start: 0.8844 (tp) cc_final: 0.8644 (tp) REVERT: C 541 ARG cc_start: 0.7876 (ttp-110) cc_final: 0.7216 (ttp-110) REVERT: C 640 LYS cc_start: 0.7636 (tttt) cc_final: 0.7342 (ttmm) REVERT: C 645 ARG cc_start: 0.6916 (tpp80) cc_final: 0.6642 (tpp-160) REVERT: C 658 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8394 (tppp) REVERT: C 665 THR cc_start: 0.7860 (m) cc_final: 0.7138 (m) REVERT: C 669 MET cc_start: 0.7618 (mtp) cc_final: 0.7187 (mtp) REVERT: C 691 ASP cc_start: 0.7302 (m-30) cc_final: 0.6966 (m-30) REVERT: D 370 ASP cc_start: 0.6993 (t0) cc_final: 0.6595 (t0) REVERT: D 414 GLN cc_start: 0.7497 (tp40) cc_final: 0.7083 (tp40) REVERT: D 590 MET cc_start: 0.7937 (tpp) cc_final: 0.7717 (tpp) REVERT: D 620 MET cc_start: 0.4681 (tmm) cc_final: 0.4380 (tmm) REVERT: D 669 MET cc_start: 0.7496 (mtp) cc_final: 0.7133 (mtp) outliers start: 16 outliers final: 14 residues processed: 312 average time/residue: 0.3371 time to fit residues: 132.0614 Evaluate side-chains 313 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 299 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 593 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112413 restraints weight = 48389.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.117753 restraints weight = 20301.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120797 restraints weight = 10245.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122523 restraints weight = 6011.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123604 restraints weight = 4120.327| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9708 Z= 0.319 Angle : 0.622 10.951 13076 Z= 0.349 Chirality : 0.035 0.193 1516 Planarity : 0.006 0.136 1684 Dihedral : 4.085 31.115 1320 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.58 % Favored : 97.17 % Rotamer: Outliers : 1.89 % Allowed : 16.48 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 3.31 (0.23), residues: 1200 helix: 2.67 (0.15), residues: 1006 sheet: None (None), residues: 0 loop : -0.55 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 555 TYR 0.010 0.002 TYR C 371 PHE 0.029 0.003 PHE D 532 TRP 0.014 0.002 TRP C 393 HIS 0.007 0.002 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.32 ( 9708) covalent geometry : angle 0.62174 / 0.35 (13076) hydrogen bonds : bond 0.05568 / 3.68 ( 911) hydrogen bonds : angle 4.16985 / 3.07 ( 2733) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 302 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7617 (tt0) cc_final: 0.7214 (tt0) REVERT: A 334 TRP cc_start: 0.7155 (m100) cc_final: 0.6244 (m100) REVERT: A 354 LEU cc_start: 0.8225 (tp) cc_final: 0.7999 (tp) REVERT: A 360 LYS cc_start: 0.8250 (tttt) cc_final: 0.7956 (tppt) REVERT: A 577 ASP cc_start: 0.7337 (m-30) cc_final: 0.7095 (t0) REVERT: A 607 GLU cc_start: 0.7135 (tt0) cc_final: 0.6799 (tt0) REVERT: A 675 GLN cc_start: 0.8088 (mp10) cc_final: 0.7809 (mp10) REVERT: A 689 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8271 (ttmm) REVERT: B 354 LEU cc_start: 0.8308 (tp) cc_final: 0.8060 (tt) REVERT: B 360 LYS cc_start: 0.8351 (tttt) cc_final: 0.8045 (ttmm) REVERT: B 577 ASP cc_start: 0.7181 (m-30) cc_final: 0.6952 (t0) REVERT: B 673 GLU cc_start: 0.7497 (tp30) cc_final: 0.7160 (tp30) REVERT: B 675 GLN cc_start: 0.8148 (mp10) cc_final: 0.7824 (mp10) REVERT: B 689 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8195 (mtmm) REVERT: C 337 MET cc_start: 0.8308 (mpp) cc_final: 0.7948 (mmp) REVERT: C 370 ASP cc_start: 0.7027 (t0) cc_final: 0.6637 (t0) REVERT: C 658 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8385 (tppp) REVERT: C 665 THR cc_start: 0.7867 (m) cc_final: 0.7228 (m) REVERT: C 669 MET cc_start: 0.7657 (mtp) cc_final: 0.7245 (mtp) REVERT: D 357 LYS cc_start: 0.8053 (tptm) cc_final: 0.7782 (tptm) REVERT: D 414 GLN cc_start: 0.7489 (tp40) cc_final: 0.7049 (tp40) REVERT: D 545 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7494 (tm-30) REVERT: D 590 MET cc_start: 0.7981 (tpp) cc_final: 0.7548 (tpp) REVERT: D 620 MET cc_start: 0.4561 (tmm) cc_final: 0.4322 (tmm) REVERT: D 658 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8357 (tppp) REVERT: D 669 MET cc_start: 0.7512 (mtp) cc_final: 0.7287 (mtp) outliers start: 20 outliers final: 17 residues processed: 314 average time/residue: 0.3560 time to fit residues: 139.5601 Evaluate side-chains 317 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 300 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 593 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122143 restraints weight = 48454.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127649 restraints weight = 20182.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130717 restraints weight = 10194.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132550 restraints weight = 6046.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133662 restraints weight = 4122.849| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9708 Z= 0.160 Angle : 0.555 10.739 13076 Z= 0.293 Chirality : 0.029 0.183 1516 Planarity : 0.005 0.132 1684 Dihedral : 3.949 31.125 1320 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.67 % Favored : 98.08 % Rotamer: Outliers : 1.04 % Allowed : 17.71 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 3.83 (0.23), residues: 1200 helix: 2.93 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : 0.08 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 555 TYR 0.005 0.001 TYR C 371 PHE 0.030 0.002 PHE D 532 TRP 0.014 0.001 TRP C 334 HIS 0.003 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 9708) covalent geometry : angle 0.55547 / 0.29 (13076) hydrogen bonds : bond 0.05140 / 3.39 ( 911) hydrogen bonds : angle 3.76024 / 2.77 ( 2733) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 296 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7473 (tt0) cc_final: 0.7055 (tt0) REVERT: A 334 TRP cc_start: 0.7095 (m100) cc_final: 0.6248 (m100) REVERT: A 354 LEU cc_start: 0.8110 (tp) cc_final: 0.7890 (tp) REVERT: A 360 LYS cc_start: 0.8199 (tttt) cc_final: 0.7909 (tppt) REVERT: A 577 ASP cc_start: 0.7284 (m-30) cc_final: 0.6881 (t70) REVERT: A 607 GLU cc_start: 0.7120 (tt0) cc_final: 0.6764 (tt0) REVERT: A 675 GLN cc_start: 0.8129 (mp10) cc_final: 0.7806 (mp10) REVERT: A 689 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8249 (ttmm) REVERT: A 699 MET cc_start: 0.7538 (tpp) cc_final: 0.7208 (tpp) REVERT: B 354 LEU cc_start: 0.8244 (tp) cc_final: 0.8014 (tt) REVERT: B 360 LYS cc_start: 0.8308 (tttt) cc_final: 0.7999 (ttmm) REVERT: B 577 ASP cc_start: 0.7130 (m-30) cc_final: 0.6899 (t0) REVERT: B 673 GLU cc_start: 0.7568 (tp30) cc_final: 0.7170 (tp30) REVERT: B 675 GLN cc_start: 0.8188 (mp10) cc_final: 0.7815 (mp10) REVERT: B 689 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8173 (mtmm) REVERT: C 335 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8600 (tm-30) REVERT: C 337 MET cc_start: 0.8313 (mpp) cc_final: 0.7961 (mmp) REVERT: C 370 ASP cc_start: 0.7008 (t0) cc_final: 0.6595 (t0) REVERT: C 541 ARG cc_start: 0.7903 (ttp-110) cc_final: 0.7204 (ttp-110) REVERT: C 640 LYS cc_start: 0.7674 (tttt) cc_final: 0.7374 (ttmm) REVERT: C 658 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8368 (tppp) REVERT: C 665 THR cc_start: 0.7885 (m) cc_final: 0.7203 (m) REVERT: C 669 MET cc_start: 0.7686 (mtp) cc_final: 0.7233 (mtp) REVERT: D 414 GLN cc_start: 0.7520 (tp40) cc_final: 0.7107 (tp40) REVERT: D 590 MET cc_start: 0.7932 (tpp) cc_final: 0.7460 (tpp) REVERT: D 620 MET cc_start: 0.4622 (tmm) cc_final: 0.4345 (tmm) REVERT: D 669 MET cc_start: 0.7560 (mtp) cc_final: 0.7164 (mtp) outliers start: 11 outliers final: 11 residues processed: 303 average time/residue: 0.3389 time to fit residues: 128.6419 Evaluate side-chains 310 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 593 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 0.0170 chunk 103 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 533 GLN D 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113227 restraints weight = 48551.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118635 restraints weight = 20216.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121717 restraints weight = 10212.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123470 restraints weight = 5983.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124523 restraints weight = 4115.973| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9708 Z= 0.247 Angle : 0.592 10.820 13076 Z= 0.324 Chirality : 0.032 0.191 1516 Planarity : 0.006 0.133 1684 Dihedral : 4.040 30.926 1320 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.42 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 18.09 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 3.56 (0.23), residues: 1200 helix: 2.80 (0.15), residues: 1006 sheet: None (None), residues: 0 loop : -0.23 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 634 TYR 0.008 0.001 TYR C 371 PHE 0.031 0.003 PHE D 532 TRP 0.010 0.002 TRP D 688 HIS 0.005 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.25 ( 9708) covalent geometry : angle 0.59222 / 0.32 (13076) hydrogen bonds : bond 0.05341 / 3.53 ( 911) hydrogen bonds : angle 3.97478 / 2.93 ( 2733) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.63 seconds wall clock time: 69 minutes 17.81 seconds (4157.81 seconds total)