Starting phenix.real_space_refine on Thu Jul 2 10:03:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m30_63594/07_2026/9m30_63594.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m30_63594/07_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_63594/07_2026/9m30_63594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m30_63594/07_2026/9m30_63594.map" model { file = "/net/cci-nas-00/data/ceres_data/9m30_63594/07_2026/9m30_63594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m30_63594/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.99, per 1000 atoms: 0.37 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: 0.76 Conformation dependent library (CDL) restraints added in 381.9 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: 0.82 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: 1.17 Time building geometry restraints manager: 0.99 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=" O5' C B -1 " pdb=" C5' C B -1 " ideal model delta sigma weight residual 1.420 1.446 -0.026 1.50e-02 4.44e+03 2.99e+00 bond pdb=" O5' G B 1 " pdb=" C5' G B 1 " ideal model delta sigma weight residual 1.420 1.446 -0.026 1.50e-02 4.44e+03 2.96e+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=" C1' G B 1 " pdb=" N9 G B 1 " ideal model delta sigma weight residual 1.475 1.454 0.021 1.50e-02 4.44e+03 2.01e+00 ... (remaining 8300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 11258 1.60 - 3.20: 160 3.20 - 4.80: 25 4.80 - 6.40: 8 6.40 - 8.00: 1 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 120.20 112.20 8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " ideal model delta sigma weight residual 102.60 99.18 3.42 1.00e+00 1.00e+00 1.17e+01 angle pdb=" C VAL A 851 " pdb=" N VAL A 852 " pdb=" CA VAL A 852 " ideal model delta sigma weight residual 120.33 122.96 -2.63 8.00e-01 1.56e+00 1.08e+01 angle pdb=" C GLN A 172 " pdb=" N THR A 173 " pdb=" CA THR A 173 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C3' A B -2 " pdb=" O3' A B -2 " pdb=" P C B -1 " ideal model delta sigma weight residual 120.20 116.13 4.07 1.50e+00 4.44e-01 7.36e+00 ... (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: 1221 0.069 - 0.138: 80 0.138 - 0.207: 4 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: 3.060 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- 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= 0.171 Angle : 0.500 8.000 11452 Z= 0.294 Chirality : 0.039 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 0.00331 / 0.17 ( 8305) covalent geometry : angle 0.50013 / 0.29 (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 : 0.284 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: 0.1292 time to fit residues: 24.4038 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 : 0.229 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.102040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085165 restraints weight = 18962.904| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.50 r_work: 0.2819 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- 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 = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 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 (8 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8305 Z= 0.212 Angle : 0.599 7.558 11452 Z= 0.330 Chirality : 0.041 0.152 1307 Planarity : 0.005 0.047 1264 Dihedral : 16.138 110.641 1682 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.91 % Allowed : 6.89 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 840 helix: 0.84 (0.23), residues: 507 sheet: -0.78 (1.66), residues: 11 loop : -1.60 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 750 TYR 0.026 0.002 TYR A 119 PHE 0.025 0.002 PHE A 420 TRP 0.014 0.002 TRP A 752 HIS 0.010 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 8305) covalent geometry : angle 0.59860 / 0.33 (11452) hydrogen bonds : bond 0.09593 / 6.55 ( 361) hydrogen bonds : angle 4.34354 / 3.09 ( 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 141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.280 Fit side-chains REVERT: A 494 TYR cc_start: 0.8133 (m-10) cc_final: 0.7921 (m-10) outliers start: 6 outliers final: 6 residues processed: 135 average time/residue: 0.1259 time to fit residues: 21.2134 Evaluate side-chains 139 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.101976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.083994 restraints weight = 29507.274| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.16 r_work: 0.2734 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8305 Z= 0.191 Angle : 0.545 7.425 11452 Z= 0.299 Chirality : 0.040 0.152 1307 Planarity : 0.004 0.047 1264 Dihedral : 16.064 110.696 1682 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.17 % Allowed : 8.19 % Favored : 90.64 % 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: 0.11 (0.29), residues: 840 helix: 1.08 (0.24), residues: 507 sheet: 0.70 (1.16), residues: 21 loop : -1.70 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 185 TYR 0.019 0.001 TYR A 119 PHE 0.025 0.002 PHE A 420 TRP 0.014 0.002 TRP A 752 HIS 0.008 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 8305) covalent geometry : angle 0.54466 / 0.30 (11452) hydrogen bonds : bond 0.08535 / 5.81 ( 361) hydrogen bonds : angle 4.13650 / 2.96 ( 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 139 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.289 Fit side-chains REVERT: A 185 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7982 (tpp80) REVERT: A 186 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7641 (ttmm) outliers start: 8 outliers final: 8 residues processed: 132 average time/residue: 0.1280 time to fit residues: 21.1733 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 : 0.170 ------------------------------------------------------------------------------- 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 469 ILE Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.102006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.083490 restraints weight = 36205.045| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.51 r_work: 0.2714 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8305 Z= 0.193 Angle : 0.538 6.682 11452 Z= 0.295 Chirality : 0.040 0.159 1307 Planarity : 0.004 0.046 1264 Dihedral : 15.999 110.812 1682 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.82 % Allowed : 8.71 % 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: 0.16 (0.29), residues: 840 helix: 1.16 (0.24), residues: 506 sheet: 0.72 (1.18), residues: 21 loop : -1.75 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.025 0.002 TYR A 119 PHE 0.024 0.002 PHE A 420 TRP 0.014 0.002 TRP A 752 HIS 0.010 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 ( 8305) covalent geometry : angle 0.53828 / 0.30 (11452) hydrogen bonds : bond 0.07833 / 5.29 ( 361) hydrogen bonds : angle 4.01033 / 2.86 ( 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 148 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.297 Fit side-chains REVERT: A 186 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7728 (ttpp) REVERT: A 601 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: A 642 TYR cc_start: 0.7768 (p90) cc_final: 0.7567 (p90) outliers start: 13 outliers final: 10 residues processed: 136 average time/residue: 0.1338 time to fit residues: 22.8871 Evaluate side-chains 145 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 421 GLU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 705 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: 0.6980 chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.103490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.086599 restraints weight = 20634.193| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.60 r_work: 0.2818 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 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 = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1662 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= 0.151 Angle : 0.500 5.819 11452 Z= 0.275 Chirality : 0.038 0.143 1307 Planarity : 0.004 0.046 1264 Dihedral : 15.931 110.424 1682 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.43 % Allowed : 9.88 % Favored : 88.69 % 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: 1.29 (0.24), residues: 508 sheet: 0.79 (1.17), residues: 21 loop : -1.73 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.018 0.001 TYR A 119 PHE 0.024 0.001 PHE A 420 TRP 0.013 0.002 TRP A 752 HIS 0.004 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8305) covalent geometry : angle 0.50043 / 0.28 (11452) hydrogen bonds : bond 0.06898 / 4.64 ( 361) hydrogen bonds : angle 3.86538 / 2.76 ( 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 146 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.212 Fit side-chains REVERT: A 186 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7685 (tttm) outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.1171 time to fit residues: 20.3598 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 : 0.268 ------------------------------------------------------------------------------- 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 411 LYS Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 473 LEU 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: 0.9980 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.102853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.084497 restraints weight = 33837.545| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.38 r_work: 0.2767 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 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 = 0.2762 r_free = 0.2762 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: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8305 Z= 0.167 Angle : 0.511 6.060 11452 Z= 0.280 Chirality : 0.039 0.145 1307 Planarity : 0.004 0.046 1264 Dihedral : 15.848 110.683 1682 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.69 % Allowed : 10.40 % Favored : 87.91 % 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: 0.32 (0.29), residues: 840 helix: 1.32 (0.24), residues: 508 sheet: 0.82 (1.17), residues: 21 loop : -1.75 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 384 TYR 0.022 0.001 TYR A 642 PHE 0.024 0.002 PHE A 420 TRP 0.013 0.002 TRP A 752 HIS 0.006 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 8305) covalent geometry : angle 0.51142 / 0.28 (11452) hydrogen bonds : bond 0.07094 / 4.76 ( 361) hydrogen bonds : angle 3.88108 / 2.76 ( 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 144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.264 Fit side-chains REVERT: A 186 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7741 (tttm) outliers start: 12 outliers final: 10 residues processed: 136 average time/residue: 0.1189 time to fit residues: 20.4506 Evaluate side-chains 141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 370 LEU 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 623 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 835 THR 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: 0.7980 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.102265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.084817 restraints weight = 25259.313| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.88 r_work: 0.2785 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8305 Z= 0.190 Angle : 0.531 5.960 11452 Z= 0.290 Chirality : 0.040 0.157 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.809 110.304 1682 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.56 % Allowed : 11.05 % Favored : 87.39 % 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: 0.32 (0.29), residues: 840 helix: 1.33 (0.24), residues: 508 sheet: 0.86 (1.19), residues: 21 loop : -1.79 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.021 0.002 TYR A 119 PHE 0.024 0.002 PHE A 420 TRP 0.013 0.002 TRP A 752 HIS 0.006 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 8305) covalent geometry : angle 0.53091 / 0.29 (11452) hydrogen bonds : bond 0.07376 / 4.97 ( 361) hydrogen bonds : angle 3.92098 / 2.79 ( 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 143 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.183 Fit side-chains REVERT: A 186 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7686 (tttm) outliers start: 11 outliers final: 11 residues processed: 135 average time/residue: 0.1262 time to fit residues: 21.2129 Evaluate side-chains 142 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 370 LEU 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 473 LEU 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: 3.9990 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.103197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086050 restraints weight = 21334.810| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.66 r_work: 0.2803 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 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 = 0.2844 r_free = 0.2844 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: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1790 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= 0.154 Angle : 0.506 7.300 11452 Z= 0.278 Chirality : 0.039 0.146 1307 Planarity : 0.004 0.045 1264 Dihedral : 15.790 110.422 1682 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.82 % Allowed : 10.79 % Favored : 87.39 % 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: 0.41 (0.29), residues: 840 helix: 1.40 (0.24), residues: 509 sheet: 0.86 (1.19), residues: 21 loop : -1.75 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.022 0.001 TYR A 642 PHE 0.024 0.001 PHE A 420 TRP 0.014 0.002 TRP A 752 HIS 0.005 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8305) covalent geometry : angle 0.50585 / 0.28 (11452) hydrogen bonds : bond 0.06850 / 4.60 ( 361) hydrogen bonds : angle 3.86306 / 2.75 ( 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 145 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.238 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 136 average time/residue: 0.1161 time to fit residues: 19.9953 Evaluate side-chains 145 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 370 LEU 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 473 LEU Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 LEU 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: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.103026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.085324 restraints weight = 29195.780| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.02 r_work: 0.2797 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8305 Z= 0.204 Angle : 0.555 8.605 11452 Z= 0.298 Chirality : 0.041 0.162 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.761 110.097 1682 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.82 % Allowed : 11.05 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.29), residues: 840 helix: 1.32 (0.24), residues: 508 sheet: 0.81 (1.19), residues: 21 loop : -1.84 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 384 TYR 0.022 0.002 TYR A 119 PHE 0.024 0.002 PHE A 420 TRP 0.013 0.002 TRP A 752 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 8305) covalent geometry : angle 0.55519 / 0.30 (11452) hydrogen bonds : bond 0.07476 / 5.03 ( 361) hydrogen bonds : angle 3.93672 / 2.80 ( 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 145 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.174 Fit side-chains REVERT: A 186 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7813 (ttmm) outliers start: 13 outliers final: 11 residues processed: 137 average time/residue: 0.1270 time to fit residues: 21.8553 Evaluate side-chains 143 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 410 GLN Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 473 LEU 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 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.085886 restraints weight = 23866.814| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.76 r_work: 0.2803 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1791 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= 0.172 Angle : 0.545 11.832 11452 Z= 0.290 Chirality : 0.040 0.154 1307 Planarity : 0.004 0.046 1264 Dihedral : 15.767 110.238 1682 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.56 % Allowed : 11.05 % Favored : 87.39 % 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: 0.34 (0.29), residues: 840 helix: 1.35 (0.24), residues: 509 sheet: 0.87 (1.20), residues: 21 loop : -1.79 (0.31), residues: 310 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 0.013 0.002 TRP A 752 HIS 0.006 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 8305) covalent geometry : angle 0.54481 / 0.29 (11452) hydrogen bonds : bond 0.07102 / 4.77 ( 361) hydrogen bonds : angle 3.90341 / 2.78 ( 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 144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.243 Fit side-chains REVERT: A 186 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7796 (ttmm) outliers start: 11 outliers final: 11 residues processed: 137 average time/residue: 0.1143 time to fit residues: 19.7987 Evaluate side-chains 144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 410 GLN Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 473 LEU 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: 0.3980 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 0.0050 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.105606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087758 restraints weight = 29160.172| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.04 r_work: 0.2797 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 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 = 0.2832 r_free = 0.2832 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: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8305 Z= 0.135 Angle : 0.509 10.659 11452 Z= 0.271 Chirality : 0.038 0.151 1307 Planarity : 0.004 0.047 1264 Dihedral : 15.674 109.953 1682 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.69 % Allowed : 10.92 % Favored : 87.39 % 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: 0.53 (0.29), residues: 840 helix: 1.50 (0.24), residues: 508 sheet: 0.93 (1.19), residues: 21 loop : -1.70 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.022 0.001 TYR A 642 PHE 0.024 0.001 PHE A 420 TRP 0.015 0.002 TRP A 752 HIS 0.004 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8305) covalent geometry : angle 0.50950 / 0.27 (11452) hydrogen bonds : bond 0.06131 / 4.11 ( 361) hydrogen bonds : angle 3.77049 / 2.69 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.60 seconds wall clock time: 34 minutes 35.82 seconds (2075.82 seconds total)