Starting phenix.real_space_refine on Wed Aug 5 02:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m30_63594/08_2026/9m30_63594.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m30_63594/08_2026/9m30_63594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m30_63594/08_2026/9m30_63594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m30_63594/08_2026/9m30_63594.map" model { file = "/net/cci-nas-00/data/ceres_data/9m30_63594/08_2026/9m30_63594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m30_63594/08_2026/9m30_63594.cif" } resolution = 3.05 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= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 1 5.21 5 S 23 5.16 5 C 4955 2.51 5 N 1379 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8027 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 844, 6932 Classifications: {'peptide': 844} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 844, 6932 Classifications: {'peptide': 844} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7070 Chain: "B" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1085 Classifications: {'RNA': 51} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p_pur': 23, 'rna3p_pyr': 21} Link IDs: {'rna2p': 7, 'rna3p': 43} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS A 5 " occ=0.70 ... (16 atoms not shown) pdb=" NZ BLYS A 5 " occ=0.30 Time building chain proxies: 2.38, per 1000 atoms: 0.30 Number of scatterers: 8027 At special positions: 0 Unit cell: (88.32, 94.76, 107.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 23 16.00 P 50 15.00 Mg 1 11.99 O 1619 8.00 N 1379 7.00 C 4955 6.00 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: 0.72 Conformation dependent library (CDL) restraints added in 338.2 milliseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 63.4% alpha, 4.1% beta 4 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 113 through 123 Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 166 through 173 removed outlier: 4.238A pdb=" N ARG A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.946A pdb=" N ASN A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.792A pdb=" N LEU A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 222 removed outlier: 3.510A pdb=" N ILE A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 3.641A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.790A pdb=" N LEU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.660A pdb=" N LYS A 359 " --> pdb=" O HIS A 355 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 399 removed outlier: 3.679A pdb=" N LYS A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ALA A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.637A pdb=" N LYS A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 445 through 473 Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.491A pdb=" N ASP A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 506 removed outlier: 3.990A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.716A pdb=" N LEU A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 585 through 591 removed outlier: 4.042A pdb=" N THR A 588 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 589 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 590 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.770A pdb=" N GLY A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.544A pdb=" N ARG A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 639 removed outlier: 3.505A pdb=" N VAL A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 647 removed outlier: 4.364A pdb=" N ASP A 647 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 712 removed outlier: 3.528A pdb=" N LYS A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 683 " --> pdb=" O TYR A 679 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 removed outlier: 3.605A pdb=" N THR A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 734 No H-bonds generated for 'chain 'A' and resid 732 through 734' Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.715A pdb=" N GLN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.702A pdb=" N ARG A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 813 removed outlier: 3.603A pdb=" N LEU A 800 " --> pdb=" O SER A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.602A pdb=" N PHE A 848 " --> pdb=" O CYS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 Processing helix chain 'A' and resid 860 through 865 removed outlier: 4.524A pdb=" N ASP A 865 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 8.681A pdb=" N LEU A 16 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 31 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 18 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 29 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER A 30 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU A 39 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 64 removed outlier: 4.928A pdb=" N ASN A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN A 71 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AA4, first strand: chain 'A' and resid 717 through 718 352 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2274 1.34 - 1.45: 1576 1.45 - 1.57: 4317 1.57 - 1.69: 100 1.69 - 1.81: 38 Bond restraints: 8305 Sorted by residual: bond pdb=" C1' G B 1 " pdb=" N9 G B 1 " ideal model delta sigma weight residual 1.483 1.454 0.029 1.50e-02 4.44e+03 3.80e+00 bond pdb=" N9 A B -4 " pdb=" C4 A B -4 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.55e+00 bond pdb=" C ILE A 846 " pdb=" N PRO A 847 " ideal model delta sigma weight residual 1.334 1.367 -0.034 2.34e-02 1.83e+03 2.06e+00 bond pdb=" O5' C B -1 " pdb=" C5' C B -1 " ideal model delta sigma weight residual 1.424 1.446 -0.022 1.60e-02 3.91e+03 1.88e+00 bond pdb=" O5' G B 1 " pdb=" C5' G B 1 " ideal model delta sigma weight residual 1.424 1.446 -0.022 1.60e-02 3.91e+03 1.86e+00 ... (remaining 8300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 11103 1.50 - 3.00: 304 3.00 - 4.50: 33 4.50 - 6.00: 9 6.00 - 7.50: 3 Bond angle restraints: 11452 Sorted by residual: angle pdb=" C3' C B -1 " pdb=" O3' C B -1 " pdb=" P G B 1 " ideal model delta sigma weight residual 119.70 112.20 7.50 1.20e+00 6.94e-01 3.91e+01 angle pdb=" O5' A B 17 " pdb=" C5' A B 17 " pdb=" C4' A B 17 " ideal model delta sigma weight residual 109.40 112.29 -2.89 8.00e-01 1.56e+00 1.30e+01 angle pdb=" O5' A B -3 " pdb=" C5' A B -3 " pdb=" C4' A B -3 " ideal model delta sigma weight residual 109.40 112.23 -2.83 8.00e-01 1.56e+00 1.25e+01 angle pdb=" O5' U B -8 " pdb=" C5' U B -8 " pdb=" C4' U B -8 " ideal model delta sigma weight residual 109.40 112.22 -2.82 8.00e-01 1.56e+00 1.24e+01 angle pdb=" O5' G B 7 " pdb=" C5' G B 7 " pdb=" C4' G B 7 " ideal model delta sigma weight residual 109.40 112.21 -2.81 8.00e-01 1.56e+00 1.23e+01 ... (remaining 11447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 4552 21.59 - 43.18: 387 43.18 - 64.77: 98 64.77 - 86.36: 24 86.36 - 107.95: 3 Dihedral angle restraints: 5064 sinusoidal: 2543 harmonic: 2521 Sorted by residual: dihedral pdb=" CG ARG A 316 " pdb=" CD ARG A 316 " pdb=" NE ARG A 316 " pdb=" CZ ARG A 316 " ideal model delta sinusoidal sigma weight residual -90.00 -134.60 44.60 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 579 " pdb=" CD ARG A 579 " pdb=" NE ARG A 579 " pdb=" CZ ARG A 579 " ideal model delta sinusoidal sigma weight residual 90.00 133.24 -43.24 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" O5' G B -12 " pdb=" C5' G B -12 " pdb=" C4' G B -12 " pdb=" C3' G B -12 " ideal model delta sinusoidal sigma weight residual 175.00 -126.13 -58.87 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1172 0.069 - 0.138: 127 0.138 - 0.207: 6 0.207 - 0.276: 0 0.276 - 0.345: 2 Chirality restraints: 1307 Sorted by residual: chirality pdb=" P C B -1 " pdb=" OP1 C B -1 " pdb=" OP2 C B -1 " pdb=" O5' C B -1 " both_signs ideal model delta sigma weight residual True 2.41 -2.75 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" P G B 1 " pdb=" OP1 G B 1 " pdb=" OP2 G B 1 " pdb=" O5' G B 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C3' C B -1 " pdb=" C4' C B -1 " pdb=" O3' C B -1 " pdb=" C2' C B -1 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1304 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 48 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 49 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 480 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO A 481 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 119 " -0.013 2.00e-02 2.50e+03 1.05e-02 2.21e+00 pdb=" CG TYR A 119 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 119 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 119 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 119 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 119 " -0.001 2.00e-02 2.50e+03 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2260 2.81 - 3.34: 6842 3.34 - 3.86: 12012 3.86 - 4.38: 14667 4.38 - 4.90: 24688 Nonbonded interactions: 60469 Sorted by model distance: nonbonded pdb=" O LYS A 306 " pdb=" O2' C B 2 " model vdw 2.292 3.040 nonbonded pdb=" O SER A 368 " pdb=" OG SER A 368 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN A 276 " pdb=" OH TYR A 296 " model vdw 2.342 3.120 nonbonded pdb=" NZ LYS A 744 " pdb=" OP1 C B -26 " model vdw 2.364 3.120 nonbonded pdb=" O SER A 639 " pdb=" OG SER A 639 " model vdw 2.368 3.040 ... (remaining 60464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.003 0.035 8305 Z= 0.180 Angle : 0.562 7.500 11452 Z= 0.357 Chirality : 0.046 0.345 1307 Planarity : 0.004 0.051 1264 Dihedral : 16.883 107.950 3434 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.27), residues: 840 helix: -0.16 (0.22), residues: 493 sheet: -0.64 (1.69), residues: 11 loop : -1.44 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.026 0.001 TYR A 119 PHE 0.025 0.001 PHE A 420 TRP 0.009 0.001 TRP A 752 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 ( 8305) covalent geometry : angle 0.56223 / 0.36 (11452) hydrogen bonds : bond 0.30039 / 20.46 ( 361) hydrogen bonds : angle 6.51112 / 4.44 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.275 Fit side-chains REVERT: A 615 CYS cc_start: 0.8085 (m) cc_final: 0.7877 (m) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1295 time to fit residues: 24.3855 Evaluate side-chains 145 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.084920 restraints weight = 18913.669| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.47 r_work: 0.2815 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8305 Z= 0.214 Angle : 0.598 7.370 11452 Z= 0.329 Chirality : 0.042 0.154 1307 Planarity : 0.005 0.047 1264 Dihedral : 16.041 108.364 1682 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.91 % Allowed : 6.63 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.29), residues: 840 helix: 0.93 (0.23), residues: 506 sheet: -0.76 (1.66), residues: 11 loop : -1.61 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 750 TYR 0.025 0.002 TYR A 119 PHE 0.026 0.002 PHE A 420 TRP 0.015 0.002 TRP A 752 HIS 0.009 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 8305) covalent geometry : angle 0.59812 / 0.33 (11452) hydrogen bonds : bond 0.10121 / 6.92 ( 361) hydrogen bonds : angle 4.40014 / 3.13 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.275 Fit side-chains REVERT: A 488 ASN cc_start: 0.7871 (p0) cc_final: 0.7637 (p0) outliers start: 6 outliers final: 6 residues processed: 136 average time/residue: 0.1220 time to fit residues: 20.8646 Evaluate side-chains 140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.086723 restraints weight = 29186.285| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.05 r_work: 0.2823 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8305 Z= 0.140 Angle : 0.503 5.950 11452 Z= 0.279 Chirality : 0.038 0.145 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.884 108.369 1682 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.04 % Allowed : 8.45 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.29), residues: 840 helix: 1.28 (0.24), residues: 506 sheet: 0.72 (1.14), residues: 21 loop : -1.69 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.031 0.001 TYR A 642 PHE 0.024 0.001 PHE A 420 TRP 0.014 0.001 TRP A 752 HIS 0.006 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 8305) covalent geometry : angle 0.50278 / 0.28 (11452) hydrogen bonds : bond 0.07431 / 5.04 ( 361) hydrogen bonds : angle 3.98110 / 2.85 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.187 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 133 average time/residue: 0.1115 time to fit residues: 18.5699 Evaluate side-chains 136 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 755 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086825 restraints weight = 35621.100| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.35 r_work: 0.2768 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8305 Z= 0.148 Angle : 0.511 9.111 11452 Z= 0.277 Chirality : 0.038 0.144 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.817 108.867 1682 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.17 % Allowed : 9.36 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 840 helix: 1.37 (0.24), residues: 507 sheet: 0.75 (1.15), residues: 21 loop : -1.63 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.023 0.001 TYR A 642 PHE 0.024 0.001 PHE A 420 TRP 0.012 0.001 TRP A 752 HIS 0.006 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8305) covalent geometry : angle 0.51124 / 0.28 (11452) hydrogen bonds : bond 0.07001 / 4.71 ( 361) hydrogen bonds : angle 3.87387 / 2.76 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.254 Fit side-chains REVERT: A 186 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7772 (ttmm) REVERT: A 705 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7701 (tp30) outliers start: 8 outliers final: 6 residues processed: 135 average time/residue: 0.1284 time to fit residues: 21.8650 Evaluate side-chains 138 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.087951 restraints weight = 20598.727| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.61 r_work: 0.2861 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8305 Z= 0.133 Angle : 0.483 5.822 11452 Z= 0.264 Chirality : 0.037 0.141 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.758 108.816 1682 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.17 % Allowed : 10.01 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 840 helix: 1.48 (0.24), residues: 508 sheet: 0.74 (1.14), residues: 21 loop : -1.61 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 384 TYR 0.023 0.001 TYR A 642 PHE 0.023 0.001 PHE A 420 TRP 0.012 0.001 TRP A 752 HIS 0.005 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8305) covalent geometry : angle 0.48295 / 0.26 (11452) hydrogen bonds : bond 0.06373 / 4.26 ( 361) hydrogen bonds : angle 3.76731 / 2.68 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.181 Fit side-chains REVERT: A 186 LYS cc_start: 0.8017 (ttpp) cc_final: 0.7728 (ttmm) REVERT: A 601 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8010 (tp30) outliers start: 8 outliers final: 6 residues processed: 135 average time/residue: 0.1093 time to fit residues: 18.6003 Evaluate side-chains 136 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 755 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 3 optimal weight: 0.0010 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.086089 restraints weight = 33848.969| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.38 r_work: 0.2786 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8305 Z= 0.137 Angle : 0.490 5.857 11452 Z= 0.267 Chirality : 0.037 0.139 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.693 108.899 1682 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.17 % Allowed : 10.79 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.29), residues: 840 helix: 1.52 (0.24), residues: 508 sheet: 0.83 (1.15), residues: 21 loop : -1.63 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.020 0.001 TYR A 642 PHE 0.022 0.001 PHE A 420 TRP 0.012 0.001 TRP A 752 HIS 0.005 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8305) covalent geometry : angle 0.49004 / 0.27 (11452) hydrogen bonds : bond 0.06342 / 4.24 ( 361) hydrogen bonds : angle 3.74256 / 2.66 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.196 Fit side-chains REVERT: A 186 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7809 (ttmm) REVERT: A 494 TYR cc_start: 0.8151 (m-10) cc_final: 0.7752 (m-10) REVERT: A 601 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8136 (tp30) outliers start: 8 outliers final: 8 residues processed: 133 average time/residue: 0.1175 time to fit residues: 19.7637 Evaluate side-chains 141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 0.0070 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.086344 restraints weight = 24952.346| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.77 r_work: 0.2784 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8305 Z= 0.179 Angle : 0.524 6.017 11452 Z= 0.283 Chirality : 0.039 0.147 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.656 108.567 1682 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.30 % Allowed : 10.92 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.29), residues: 840 helix: 1.54 (0.24), residues: 502 sheet: 0.83 (1.16), residues: 21 loop : -1.71 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.020 0.002 TYR A 642 PHE 0.023 0.002 PHE A 420 TRP 0.011 0.001 TRP A 752 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 8305) covalent geometry : angle 0.52389 / 0.28 (11452) hydrogen bonds : bond 0.07097 / 4.76 ( 361) hydrogen bonds : angle 3.84729 / 2.74 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.271 Fit side-chains REVERT: A 186 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7778 (ttmm) REVERT: A 494 TYR cc_start: 0.8146 (m-10) cc_final: 0.7749 (m-10) REVERT: A 601 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8087 (tp30) outliers start: 9 outliers final: 7 residues processed: 135 average time/residue: 0.1069 time to fit residues: 18.3303 Evaluate side-chains 138 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.086124 restraints weight = 21156.284| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.53 r_work: 0.2840 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8305 Z= 0.195 Angle : 0.552 11.176 11452 Z= 0.294 Chirality : 0.041 0.209 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.651 108.258 1682 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.30 % Allowed : 11.05 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 840 helix: 1.41 (0.24), residues: 508 sheet: 0.88 (1.19), residues: 21 loop : -1.74 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.021 0.002 TYR A 119 PHE 0.024 0.002 PHE A 420 TRP 0.011 0.002 TRP A 752 HIS 0.008 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 8305) covalent geometry : angle 0.55238 / 0.29 (11452) hydrogen bonds : bond 0.07341 / 4.94 ( 361) hydrogen bonds : angle 3.89149 / 2.77 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.199 Fit side-chains REVERT: A 186 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7807 (ttmm) outliers start: 9 outliers final: 8 residues processed: 134 average time/residue: 0.1092 time to fit residues: 18.3565 Evaluate side-chains 138 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085028 restraints weight = 29500.780| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.13 r_work: 0.2788 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8305 Z= 0.178 Angle : 0.543 11.169 11452 Z= 0.289 Chirality : 0.040 0.155 1307 Planarity : 0.004 0.046 1264 Dihedral : 15.613 108.239 1682 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.43 % Allowed : 10.92 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 840 helix: 1.41 (0.24), residues: 509 sheet: 0.86 (1.19), residues: 21 loop : -1.74 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.020 0.001 TYR A 642 PHE 0.025 0.002 PHE A 420 TRP 0.012 0.001 TRP A 752 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 8305) covalent geometry : angle 0.54345 / 0.29 (11452) hydrogen bonds : bond 0.07141 / 4.79 ( 361) hydrogen bonds : angle 3.88239 / 2.77 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.274 Fit side-chains REVERT: A 186 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7797 (ttmm) outliers start: 10 outliers final: 10 residues processed: 134 average time/residue: 0.1209 time to fit residues: 20.4066 Evaluate side-chains 140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086891 restraints weight = 23644.476| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.69 r_work: 0.2815 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8305 Z= 0.162 Angle : 0.517 10.734 11452 Z= 0.279 Chirality : 0.039 0.148 1307 Planarity : 0.004 0.046 1264 Dihedral : 15.460 108.239 1682 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.43 % Allowed : 10.40 % Favored : 88.17 % 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: 0.50 (0.29), residues: 840 helix: 1.47 (0.24), residues: 508 sheet: 0.87 (1.19), residues: 21 loop : -1.71 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 384 TYR 0.020 0.001 TYR A 642 PHE 0.026 0.001 PHE A 420 TRP 0.012 0.001 TRP A 752 HIS 0.006 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 8305) covalent geometry : angle 0.51691 / 0.28 (11452) hydrogen bonds : bond 0.06818 / 4.56 ( 361) hydrogen bonds : angle 3.80685 / 2.71 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.241 Fit side-chains REVERT: A 186 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7829 (ttmm) outliers start: 10 outliers final: 10 residues processed: 133 average time/residue: 0.1173 time to fit residues: 19.5819 Evaluate side-chains 140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 76 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088291 restraints weight = 29075.078| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.00 r_work: 0.2835 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8305 Z= 0.130 Angle : 0.491 10.208 11452 Z= 0.266 Chirality : 0.037 0.140 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.355 108.258 1682 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.30 % Allowed : 10.66 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.29), residues: 840 helix: 1.57 (0.24), residues: 508 sheet: 0.89 (1.18), residues: 21 loop : -1.66 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.021 0.001 TYR A 642 PHE 0.025 0.001 PHE A 420 TRP 0.014 0.001 TRP A 752 HIS 0.004 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 8305) covalent geometry : angle 0.49125 / 0.27 (11452) hydrogen bonds : bond 0.06158 / 4.11 ( 361) hydrogen bonds : angle 3.72500 / 2.65 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1834.13 seconds wall clock time: 31 minutes 59.62 seconds (1919.62 seconds total)